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* checking for file ‘tidybulk/DESCRIPTION’ ... OK
* preparing ‘tidybulk’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* building the PDF package manual
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[]\T1/ptm/m/n/10 Underlying cus-tom method: data fil-ter(n_aggr > 1) group_by(!
!.sample,!!.transcript) dplyr::mutate(!!.abundance
[7]
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[]\T1/ptm/m/n/10 <[`tidy-eval`][dplyr_tidy_eval]> Vari-ables, or func-tions or
vari-ables. Use [desc()]
[8]
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[]\T1/zi4/m/n/9 tidybulk::se_mini |> tidybulk() |> select(feature, count) |> h
ead() |> as_matrix(rownames=feature)[]
[9] [10] [11] [12] [13] [14] [15]
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[]\T1/zi4/m/n/9 tidybulk::se_mini |> tidybulk() |>filter(sample=="SRR1740034")
|> deconvolve_cellularity(sample, feature, count, cores = 1)[]
[17] [18] [19] [20] [21] [22] [23] [24]
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[]\T1/ptm/m/n/10 When `.drop = TRUE`, empty groups are dropped. See [group_by_d
rop_default()]
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[]\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min-
i-mum_counts, group = string_factor_of_interest,
[27] [28] [29]
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
[30] [31] [32]
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[]\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min-
i-mum_counts, group = string_factor_of_interest,
[33] [34] [35]
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
[36] [37] [38] [39] [40] [41]
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[]\T1/zi4/m/n/9 counts.MDS.rotated = rotate_dimensions(counts.MDS, \TS1/cmtt/
m/n/9 `\T1/zi4/m/n/9 Dim1\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , \TS1/cmtt/m/n/9 `\T1/
zi4/m/n/9 Dim2\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , rotation_degrees = 45, .element
= sample)[]
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[]\T1/ptm/m/n/10 Underlying method edgeR::calcNormFactors(.data, method = c("TM
M","TMMwsp","RLE","upperquartile"))
[54] [55] [56]
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[]\T1/zi4/m/n/9 tidybulk::se_mini |> tidybulk() |> as_tibble() |> symbol_to_en
trez(.transcript = feature, .sample = sample)[]
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[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther "edgeR_quasi_likelihood" (i.e.,
QLF), "edgeR_likelihood_ratio"
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\T1/ptm/m/n/10 (i.e., LRT), "edger_robust_likelihood_ratio", "DE-Seq2", "limma_
voom", "limma_voom_sample_weights"
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\T1/ptm/m/n/10 and limma-voom (i.e., edgeR::calcNormFactors; "TMM","TMMwsp","RL
E","upperquartile").
[60]
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\T1/zi4/m/n/10 btp616$[][]\T1/ptm/m/n/10 , limma-voom [][]$\T1/zi4/m/n/10 https
: / / doi . org / 10 . 1186 / gb-[]2014-[]15-[]2-[]r29$[][]\T1/ptm/m/n/10 , li
mma_voom_sample_weights
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[][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1093 / nar / gkv412$[][] \T1/p
tm/m/n/10 or DE-Seq2 [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1186 / s1
3059-[]014-[]0550-[]8$[][]
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[]\T1/ptm/m/n/10 # Fil-ter keep_abundant( fac-tor_of_interest = !!(as.symbol(pa
rse_formula(.formula)[1])), min-i-mum_counts
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[]\T1/ptm/m/n/10 # For-mat se-lect(!!.transcript,!!.sample,!!.abundance) spread
(!!.sample,!!.abundance) as_matrix(rownames
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[]\T1/ptm/m/n/10 # edgeR edgeR::DGEList(counts = .) edgeR::calcNormFactors(meth
od = scal-ing_method) edgeR::estimateDisp(design)
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[]\T1/ptm/m/n/10 # Fit edgeR::glmQLFit(design) edgeR::glmQLFTest(coef = 2, con-
trast = my_contrasts) // or glmLRT
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[]\T1/ptm/m/n/10 Underlying method for DE-Seq2 frame-work: keep_abundant( fac-t
or_of_interest = !!as.symbol(parse_formula(.formula)[[1]]),
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\T1/ptm/m/n/10 forms: mul-ti-vari-able (rec-om-mended) or uni-vari-able Re-spec
-tively: \"fac-tor_of_interest
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[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther \"ciber-sort\", \"epic\" or \"ll
sr\". The re-gres-sion method
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\T1/ptm/m/n/10 script, !!.abun-dance, method=method, ref-er-ence = ref-er-ence,
ac-tion="get", ... ) [..] betareg::betareg(.my_formula,
[64]
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\T1/ptm/m/n/10 !!.abun-dance, method=method, ref-er-ence = ref-er-ence, ac-tion
="get", ... ) [..] mu-tate(.proportion_0_corrected
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[]\T1/ptm/m/n/10 This wrap-per ex-e-cutes en-sem-ble gene en-rich-ment anal-y-s
es of the dataset us-ing EGSEA (DOI:0.12688/f1000research.12544.1)
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[]\T1/ptm/m/n/10 # Make sure tran-script names are ad-ja-cent [...] as_matrix(r
ownames = !!.en-trez) edgeR::DGEList(counts
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[]\T1/ptm/m/n/10 idx = buil-dIdx(entrezIDs = row-names(dge), species = species,
msigdb.gsets = msigdb.gsets, kegg.exclude
[68]
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[]\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini |> tidybulk() |> as_tibble() |>
symbol_to_entrez( .transcript = feature, .sample = sample)[]
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[]\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[]
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[] \T1/zi4/m/n/9 gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6"
, "c7", "kegg_disease", "kegg_metabolism", "kegg_signaling"),[]
[69] [70]
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[]\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini |> tidybulk() |> as_tibble() |>
symbol_to_entrez( .transcript = feature, .sample = sample)[]
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[]\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[]
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[]\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF
4", "PLCH2", "PADI4", "PAX7"))[]
[71] [72] [73]
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[]\T1/ptm/m/n/10 # Ex-e-cute cal-cu-la-tion nest(data = -gs_cat) mu-tate(fit =
map( data, ~ clus-ter-Pro-filer::GSEA( my_entrez_rank,
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[]\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini |> tidybulk() |> as_tibble() |>
symbol_to_entrez( .transcript = feature, .sample = sample)[]
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[]\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[]
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[]\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF
4", "PLCH2", "PADI4", "PAX7"))[]
[74] [75]
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\T1/ptm/m/n/10 forms: mul-ti-vari-able (rec-om-mended) or uni-vari-able Re-spec
-tively: \"fac-tor_of_interest
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[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther \"ciber-sort\", \"epic\" or \"ll
sr\". The re-gres-sion method
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[]\T1/ptm/m/n/10 Underlying cus-tom method: data fil-ter(n_aggr > 1) group_by(!
!.sample,!!.transcript) dplyr::mutate(!!.abundance
[8]
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vari-ables. Use [desc()]
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[]\T1/zi4/m/n/9 tidybulk::se_mini |> tidybulk() |> select(feature, count) |> h
ead() |> as_matrix(rownames=feature)[]
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[]\T1/zi4/m/n/9 tidybulk::se_mini |> tidybulk() |>filter(sample=="SRR1740034")
|> deconvolve_cellularity(sample, feature, count, cores = 1)[]
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[]\T1/ptm/m/n/10 When `.drop = TRUE`, empty groups are dropped. See [group_by_d
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[]\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min-
i-mum_counts, group = string_factor_of_interest,
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
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[]\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min-
i-mum_counts, group = string_factor_of_interest,
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
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[]\T1/zi4/m/n/9 counts.MDS.rotated = rotate_dimensions(counts.MDS, \TS1/cmtt/
m/n/9 `\T1/zi4/m/n/9 Dim1\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , \TS1/cmtt/m/n/9 `\T1/
zi4/m/n/9 Dim2\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , rotation_degrees = 45, .element
= sample)[]
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[]\T1/ptm/m/n/10 Underlying method edgeR::calcNormFactors(.data, method = c("TM
M","TMMwsp","RLE","upperquartile"))
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[]\T1/zi4/m/n/9 tidybulk::se_mini |> tidybulk() |> as_tibble() |> symbol_to_en
trez(.transcript = feature, .sample = sample)[]
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[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther "edgeR_quasi_likelihood" (i.e.,
QLF), "edgeR_likelihood_ratio"
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\T1/ptm/m/n/10 (i.e., LRT), "edger_robust_likelihood_ratio", "DE-Seq2", "limma_
voom", "limma_voom_sample_weights"
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\T1/ptm/m/n/10 and limma-voom (i.e., edgeR::calcNormFactors; "TMM","TMMwsp","RL
E","upperquartile").
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\T1/zi4/m/n/10 btp616$[][]\T1/ptm/m/n/10 , limma-voom [][]$\T1/zi4/m/n/10 https
: / / doi . org / 10 . 1186 / gb-[]2014-[]15-[]2-[]r29$[][]\T1/ptm/m/n/10 , li
mma_voom_sample_weights
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[][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1093 / nar / gkv412$[][] \T1/p
tm/m/n/10 or DE-Seq2 [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1186 / s1
3059-[]014-[]0550-[]8$[][]
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[]\T1/ptm/m/n/10 # Fil-ter keep_abundant( fac-tor_of_interest = !!(as.symbol(pa
rse_formula(.formula)[1])), min-i-mum_counts
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[]\T1/ptm/m/n/10 # For-mat se-lect(!!.transcript,!!.sample,!!.abundance) spread
(!!.sample,!!.abundance) as_matrix(rownames
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[]\T1/ptm/m/n/10 # edgeR edgeR::DGEList(counts = .) edgeR::calcNormFactors(meth
od = scal-ing_method) edgeR::estimateDisp(design)
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[]\T1/ptm/m/n/10 # Fit edgeR::glmQLFit(design) edgeR::glmQLFTest(coef = 2, con-
trast = my_contrasts) // or glmLRT
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[]\T1/ptm/m/n/10 Underlying method for DE-Seq2 frame-work: keep_abundant( fac-t
or_of_interest = !!as.symbol(parse_formula(.formula)[[1]]),
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\T1/ptm/m/n/10 forms: mul-ti-vari-able (rec-om-mended) or uni-vari-able Re-spec
-tively: \"fac-tor_of_interest
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[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther \"ciber-sort\", \"epic\" or \"ll
sr\". The re-gres-sion method
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\T1/ptm/m/n/10 script, !!.abun-dance, method=method, ref-er-ence = ref-er-ence,
ac-tion="get", ... ) [..] betareg::betareg(.my_formula,
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\T1/ptm/m/n/10 !!.abun-dance, method=method, ref-er-ence = ref-er-ence, ac-tion
="get", ... ) [..] mu-tate(.proportion_0_corrected
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[]\T1/ptm/m/n/10 This wrap-per ex-e-cutes en-sem-ble gene en-rich-ment anal-y-s
es of the dataset us-ing EGSEA (DOI:0.12688/f1000research.12544.1)
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[]\T1/ptm/m/n/10 # Make sure tran-script names are ad-ja-cent [...] as_matrix(r
ownames = !!.en-trez) edgeR::DGEList(counts
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[]\T1/ptm/m/n/10 idx = buil-dIdx(entrezIDs = row-names(dge), species = species,
msigdb.gsets = msigdb.gsets, kegg.exclude
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[]\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini |> tidybulk() |> as_tibble() |>
symbol_to_entrez( .transcript = feature, .sample = sample)[]
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[]\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[]
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[] \T1/zi4/m/n/9 gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6"
, "c7", "kegg_disease", "kegg_metabolism", "kegg_signaling"),[]
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[]\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini |> tidybulk() |> as_tibble() |>
symbol_to_entrez( .transcript = feature, .sample = sample)[]
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[]\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[]
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[]\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF
4", "PLCH2", "PADI4", "PAX7"))[]
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[]\T1/ptm/m/n/10 # Ex-e-cute cal-cu-la-tion nest(data = -gs_cat) mu-tate(fit =
map( data, ~ clus-ter-Pro-filer::GSEA( my_entrez_rank,
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symbol_to_entrez( .transcript = feature, .sample = sample)[]
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[]\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
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[]\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF
4", "PLCH2", "PADI4", "PAX7"))[]
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[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther \"ciber-sort\", \"epic\" or \"ll
sr\". The re-gres-sion method
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!.sample,!!.transcript) dplyr::mutate(!!.abundance
[8]
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[]\T1/ptm/m/n/10 <[`tidy-eval`][dplyr_tidy_eval]> Vari-ables, or func-tions or
vari-ables. Use [desc()]
[9]
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[]\T1/zi4/m/n/9 tidybulk::se_mini |> tidybulk() |> select(feature, count) |> h
ead() |> as_matrix(rownames=feature)[]
[10] [11] [12] [13] [14] [15] [16]
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[]\T1/zi4/m/n/9 tidybulk::se_mini |> tidybulk() |>filter(sample=="SRR1740034")
|> deconvolve_cellularity(sample, feature, count, cores = 1)[]
[18] [19] [20] [21] [22] [23] [24] [25]
Overfull \hbox (7.27914pt too wide) in paragraph at lines 1455--1457
[]\T1/ptm/m/n/10 When `.drop = TRUE`, empty groups are dropped. See [group_by_d
rop_default()]
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/t1cmtt.fd)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/ts1cmtt.fd) [26] [27]
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[]\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min-
i-mum_counts, group = string_factor_of_interest,
[28] [29] [30]
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
[31] [32] [33]
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[]\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min-
i-mum_counts, group = string_factor_of_interest,
[34] [35] [36]
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
[37] [38] [39] [40] [41] [42]
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[44] [45] [46] [47] [48] [49] [50] [51]
Overfull \hbox (79.64253pt too wide) in paragraph at lines 2964--2964
[]\T1/zi4/m/n/9 counts.MDS.rotated = rotate_dimensions(counts.MDS, \TS1/cmtt/
m/n/9 `\T1/zi4/m/n/9 Dim1\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , \TS1/cmtt/m/n/9 `\T1/
zi4/m/n/9 Dim2\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , rotation_degrees = 45, .element
= sample)[]
[52] [53]
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[]\T1/ptm/m/n/10 Underlying method edgeR::calcNormFactors(.data, method = c("TM
M","TMMwsp","RLE","upperquartile"))
[55] [56] [57]
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[]\T1/zi4/m/n/9 tidybulk::se_mini |> tidybulk() |> as_tibble() |> symbol_to_en
trez(.transcript = feature, .sample = sample)[]
[58] [59]
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[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther "edgeR_quasi_likelihood" (i.e.,
QLF), "edgeR_likelihood_ratio"
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\T1/ptm/m/n/10 (i.e., LRT), "edger_robust_likelihood_ratio", "DE-Seq2", "limma_
voom", "limma_voom_sample_weights"
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\T1/ptm/m/n/10 and limma-voom (i.e., edgeR::calcNormFactors; "TMM","TMMwsp","RL
E","upperquartile").
[61]
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\T1/zi4/m/n/10 btp616$[][]\T1/ptm/m/n/10 , limma-voom [][]$\T1/zi4/m/n/10 https
: / / doi . org / 10 . 1186 / gb-[]2014-[]15-[]2-[]r29$[][]\T1/ptm/m/n/10 , li
mma_voom_sample_weights
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[][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1093 / nar / gkv412$[][] \T1/p
tm/m/n/10 or DE-Seq2 [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1186 / s1
3059-[]014-[]0550-[]8$[][]
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[]\T1/ptm/m/n/10 # Fil-ter keep_abundant( fac-tor_of_interest = !!(as.symbol(pa
rse_formula(.formula)[1])), min-i-mum_counts
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[]\T1/ptm/m/n/10 # For-mat se-lect(!!.transcript,!!.sample,!!.abundance) spread
(!!.sample,!!.abundance) as_matrix(rownames
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[]\T1/ptm/m/n/10 # edgeR edgeR::DGEList(counts = .) edgeR::calcNormFactors(meth
od = scal-ing_method) edgeR::estimateDisp(design)
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[]\T1/ptm/m/n/10 # Fit edgeR::glmQLFit(design) edgeR::glmQLFTest(coef = 2, con-
trast = my_contrasts) // or glmLRT
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[]\T1/ptm/m/n/10 Underlying method for DE-Seq2 frame-work: keep_abundant( fac-t
or_of_interest = !!as.symbol(parse_formula(.formula)[[1]]),
[62] [63]
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\T1/ptm/m/n/10 forms: mul-ti-vari-able (rec-om-mended) or uni-vari-able Re-spec
-tively: \"fac-tor_of_interest
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[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther \"ciber-sort\", \"epic\" or \"ll
sr\". The re-gres-sion method
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\T1/ptm/m/n/10 script, !!.abun-dance, method=method, ref-er-ence = ref-er-ence,
ac-tion="get", ... ) [..] betareg::betareg(.my_formula,
[65]
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\T1/ptm/m/n/10 !!.abun-dance, method=method, ref-er-ence = ref-er-ence, ac-tion
="get", ... ) [..] mu-tate(.proportion_0_corrected
[66] [67]
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[]\T1/ptm/m/n/10 This wrap-per ex-e-cutes en-sem-ble gene en-rich-ment anal-y-s
es of the dataset us-ing EGSEA (DOI:0.12688/f1000research.12544.1)
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[]\T1/ptm/m/n/10 # Make sure tran-script names are ad-ja-cent [...] as_matrix(r
ownames = !!.en-trez) edgeR::DGEList(counts
Overfull \hbox (20.2169pt too wide) in paragraph at lines 3951--3953
[]\T1/ptm/m/n/10 idx = buil-dIdx(entrezIDs = row-names(dge), species = species,
msigdb.gsets = msigdb.gsets, kegg.exclude
[69]
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[]\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini |> tidybulk() |> as_tibble() |>
symbol_to_entrez( .transcript = feature, .sample = sample)[]
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[]\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[]
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[] \T1/zi4/m/n/9 gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6"
, "c7", "kegg_disease", "kegg_metabolism", "kegg_signaling"),[]
[70] [71]
Overfull \hbox (123.73795pt too wide) in paragraph at lines 4146--4146
[]\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini |> tidybulk() |> as_tibble() |>
symbol_to_entrez( .transcript = feature, .sample = sample)[]
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[]\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[]
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[]\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF
4", "PLCH2", "PADI4", "PAX7"))[]
[72] [73] [74]
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[]\T1/ptm/m/n/10 # Ex-e-cute cal-cu-la-tion nest(data = -gs_cat) mu-tate(fit =
map( data, ~ clus-ter-Pro-filer::GSEA( my_entrez_rank,
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[]\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini |> tidybulk() |> as_tibble() |>
symbol_to_entrez( .transcript = feature, .sample = sample)[]
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[]\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[]
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[]\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF
4", "PLCH2", "PADI4", "PAX7"))[]
[75] [76]
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\T1/ptm/m/n/10 forms: mul-ti-vari-able (rec-om-mended) or uni-vari-able Re-spec
-tively: \"fac-tor_of_interest
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[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther \"ciber-sort\", \"epic\" or \"ll
sr\". The re-gres-sion method
[77] [78] [79] [80] [81]
(/private/tmp/RtmpOcEnXs/Rbuild70af1c6205f6/tidybulk/.Rd2pdf28847/Rd2.ind
[82]
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[]| \T1/zi4/m/n/10 vignette_manuscript_signature_boxplot\T1/ptm/m/n/10 ,
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[]| \T1/zi4/m/n/10 vignette_manuscript_signature_tsne\T1/ptm/m/n/10 ,
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[]| \T1/zi4/m/n/10 vignette_manuscript_signature_tsne2\T1/ptm/m/n/10 ,
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(Font) using `T1/zi4/m/n' instead on input line 27.
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[]\T1/zi4/m/it/10 adjust_abundance,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 adjust_abundance,SummarizedExperiment-method
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[]\T1/zi4/m/it/10 aggregate_duplicates,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 aggregate_duplicates,spec_tbl_df-method
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[]\T1/zi4/m/it/10 aggregate_duplicates,SummarizedExperiment-method
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[]\T1/zi4/m/it/10 as_SummarizedExperiment,spec_tbl_df-method
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[]\T1/zi4/m/it/10 as_SummarizedExperiment,tidybulk-method
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[]\T1/zi4/m/it/10 cluster_elements,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 cluster_elements,SummarizedExperiment-method
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[]\T1/zi4/m/it/10 deconvolve_cellularity,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 deconvolve_cellularity,spec_tbl_df-method
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[]\T1/zi4/m/it/10 deconvolve_cellularity,SummarizedExperiment-method
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[]\T1/zi4/m/it/10 deconvolve_cellularity,tidybulk-method
[83]
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[]\T1/zi4/m/it/10 describe_transcript,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 describe_transcript,spec_tbl_df-method
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[]\T1/zi4/m/it/10 describe_transcript,SummarizedExperiment-method
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[]\T1/zi4/m/it/10 fill_missing_abundance,spec_tbl_df-method
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[]\T1/zi4/m/it/10 fill_missing_abundance,tidybulk-method
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[]\T1/zi4/m/it/10 get_bibliography,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 get_bibliography,SummarizedExperiment-method
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[]\T1/zi4/m/it/10 identify_abundant,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 identify_abundant,SummarizedExperiment-method
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[]\T1/zi4/m/it/10 impute_missing_abundance,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 impute_missing_abundance,tbl_df-method
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[]\T1/zi4/m/it/10 impute_missing_abundance,tidybulk-method
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[]\T1/zi4/m/it/10 keep_abundant,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 keep_abundant,SummarizedExperiment-method
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[]\T1/zi4/m/it/10 keep_variable,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 keep_variable,SummarizedExperiment-method
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[]\T1/zi4/m/it/10 pivot_sample,RangedSummarizedExperiment-method
[84]
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[]\T1/zi4/m/it/10 pivot_sample,SummarizedExperiment-method
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[]\T1/zi4/m/it/10 pivot_transcript,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 pivot_transcript,SummarizedExperiment-method
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[]\T1/zi4/m/it/10 reduce_dimensions,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 reduce_dimensions,SummarizedExperiment-method
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[]\T1/zi4/m/it/10 remove_redundancy,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 remove_redundancy,SummarizedExperiment-method
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[]\T1/zi4/m/it/10 rotate_dimensions,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 rotate_dimensions,SummarizedExperiment-method
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[]\T1/zi4/m/it/10 scale_abundance,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 scale_abundance,SummarizedExperiment-method
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[]\T1/zi4/m/it/10 test_differential_abundance,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 test_differential_abundance,tbl_df-method
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[]\T1/zi4/m/it/10 test_differential_abundance,tidybulk-method
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[]\T1/zi4/m/it/10 test_differential_cellularity,RangedSummarizedExperiment-meth
od
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\T1/ptm/m/it/10 (\T1/zi4/m/it/10 test_differential_cellularity\T1/ptm/m/it/10 )
\T1/ptm/m/n/10 ,
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[]\T1/zi4/m/it/10 test_differential_cellularity,spec_tbl_df-method
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\T1/ptm/m/it/10 (\T1/zi4/m/it/10 test_differential_cellularity\T1/ptm/m/it/10 )
\T1/ptm/m/n/10 ,
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[]\T1/zi4/m/it/10 test_differential_cellularity,SummarizedExperiment-method
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\T1/ptm/m/it/10 (\T1/zi4/m/it/10 test_differential_cellularity\T1/ptm/m/it/10 )
\T1/ptm/m/n/10 ,
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[]\T1/zi4/m/it/10 test_differential_cellularity,tbl_df-method
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\T1/ptm/m/it/10 (\T1/zi4/m/it/10 test_differential_cellularity\T1/ptm/m/it/10 )
\T1/ptm/m/n/10 ,
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[]\T1/zi4/m/it/10 test_differential_cellularity,tidybulk-method
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\T1/ptm/m/it/10 (\T1/zi4/m/it/10 test_differential_cellularity\T1/ptm/m/it/10 )
\T1/ptm/m/n/10 ,
[85]
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[]\T1/zi4/m/it/10 test_gene_enrichment,RangedSummarizedExperiment-method
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[]\T1/zi4/m/it/10 test_gene_overrepresentation,RangedSummarizedExperiment-metho
d
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[]\T1/zi4/m/it/10 test_gene_overrepresentation,tidybulk-method
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[]\T1/zi4/m/it/10 test_stratification_cellularity,RangedSummarizedExperiment-me
thod
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[]\T1/ptm/m/n/10 Underlying cus-tom method: data fil-ter(n_aggr > 1) group_by(!
!.sample,!!.transcript) dplyr::mutate(!!.abundance
[8]
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[]\T1/ptm/m/n/10 <[`tidy-eval`][dplyr_tidy_eval]> Vari-ables, or func-tions or
vari-ables. Use [desc()]
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[]\T1/zi4/m/n/9 tidybulk::se_mini |> tidybulk() |> select(feature, count) |> h
ead() |> as_matrix(rownames=feature)[]
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[]\T1/zi4/m/n/9 tidybulk::se_mini |> tidybulk() |>filter(sample=="SRR1740034")
|> deconvolve_cellularity(sample, feature, count, cores = 1)[]
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[]\T1/ptm/m/n/10 When `.drop = TRUE`, empty groups are dropped. See [group_by_d
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[]\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min-
i-mum_counts, group = string_factor_of_interest,
[28] [29] [30]
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
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[]\T1/ptm/m/n/10 Underlying method: edgeR::filterByExpr( data, min.count = min-
i-mum_counts, group = string_factor_of_interest,
[34] [35] [36]
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[]\T1/zi4/m/n/9 annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble(
) %>% distinct(sample) %>% mutate(source = "AU")[]
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[]\T1/zi4/m/n/9 counts.MDS.rotated = rotate_dimensions(counts.MDS, \TS1/cmtt/
m/n/9 `\T1/zi4/m/n/9 Dim1\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , \TS1/cmtt/m/n/9 `\T1/
zi4/m/n/9 Dim2\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , rotation_degrees = 45, .element
= sample)[]
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[]\T1/ptm/m/n/10 Underlying method edgeR::calcNormFactors(.data, method = c("TM
M","TMMwsp","RLE","upperquartile"))
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[]\T1/zi4/m/n/9 tidybulk::se_mini |> tidybulk() |> as_tibble() |> symbol_to_en
trez(.transcript = feature, .sample = sample)[]
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[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther "edgeR_quasi_likelihood" (i.e.,
QLF), "edgeR_likelihood_ratio"
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voom", "limma_voom_sample_weights"
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E","upperquartile").
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\T1/zi4/m/n/10 btp616$[][]\T1/ptm/m/n/10 , limma-voom [][]$\T1/zi4/m/n/10 https
: / / doi . org / 10 . 1186 / gb-[]2014-[]15-[]2-[]r29$[][]\T1/ptm/m/n/10 , li
mma_voom_sample_weights
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[][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1093 / nar / gkv412$[][] \T1/p
tm/m/n/10 or DE-Seq2 [][]$\T1/zi4/m/n/10 https : / / doi . org / 10 . 1186 / s1
3059-[]014-[]0550-[]8$[][]
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[]\T1/ptm/m/n/10 # Fil-ter keep_abundant( fac-tor_of_interest = !!(as.symbol(pa
rse_formula(.formula)[1])), min-i-mum_counts
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[]\T1/ptm/m/n/10 # For-mat se-lect(!!.transcript,!!.sample,!!.abundance) spread
(!!.sample,!!.abundance) as_matrix(rownames
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[]\T1/ptm/m/n/10 # edgeR edgeR::DGEList(counts = .) edgeR::calcNormFactors(meth
od = scal-ing_method) edgeR::estimateDisp(design)
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[]\T1/ptm/m/n/10 # Fit edgeR::glmQLFit(design) edgeR::glmQLFTest(coef = 2, con-
trast = my_contrasts) // or glmLRT
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[]\T1/ptm/m/n/10 Underlying method for DE-Seq2 frame-work: keep_abundant( fac-t
or_of_interest = !!as.symbol(parse_formula(.formula)[[1]]),
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\T1/ptm/m/n/10 forms: mul-ti-vari-able (rec-om-mended) or uni-vari-able Re-spec
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[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther \"ciber-sort\", \"epic\" or \"ll
sr\". The re-gres-sion method
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\T1/ptm/m/n/10 script, !!.abun-dance, method=method, ref-er-ence = ref-er-ence,
ac-tion="get", ... ) [..] betareg::betareg(.my_formula,
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\T1/ptm/m/n/10 !!.abun-dance, method=method, ref-er-ence = ref-er-ence, ac-tion
="get", ... ) [..] mu-tate(.proportion_0_corrected
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[]\T1/ptm/m/n/10 This wrap-per ex-e-cutes en-sem-ble gene en-rich-ment anal-y-s
es of the dataset us-ing EGSEA (DOI:0.12688/f1000research.12544.1)
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[]\T1/ptm/m/n/10 # Make sure tran-script names are ad-ja-cent [...] as_matrix(r
ownames = !!.en-trez) edgeR::DGEList(counts
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[]\T1/ptm/m/n/10 idx = buil-dIdx(entrezIDs = row-names(dge), species = species,
msigdb.gsets = msigdb.gsets, kegg.exclude
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[]\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini |> tidybulk() |> as_tibble() |>
symbol_to_entrez( .transcript = feature, .sample = sample)[]
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[]\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[]
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[] \T1/zi4/m/n/9 gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6"
, "c7", "kegg_disease", "kegg_metabolism", "kegg_signaling"),[]
[70] [71]
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[]\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini |> tidybulk() |> as_tibble() |>
symbol_to_entrez( .transcript = feature, .sample = sample)[]
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[]\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[]
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[]\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF
4", "PLCH2", "PADI4", "PAX7"))[]
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[]\T1/ptm/m/n/10 # Ex-e-cute cal-cu-la-tion nest(data = -gs_cat) mu-tate(fit =
map( data, ~ clus-ter-Pro-filer::GSEA( my_entrez_rank,
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[]\T1/zi4/m/n/9 df_entrez = tidybulk::se_mini |> tidybulk() |> as_tibble() |>
symbol_to_entrez( .transcript = feature, .sample = sample)[]
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[]\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
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[]\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = feature %in% c("TNFRSF
4", "PLCH2", "PADI4", "PAX7"))[]
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[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther \"ciber-sort\", \"epic\" or \"ll
sr\". The re-gres-sion method
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