mist:methylation inference for single-cell along trajectory
7 January 2025
Contents
- 0.1 Introduction
- 0.2 Installation
- 0.3 Example Workflow for Single-Group Analysis
- 1 Step 1: Load Example Data
- 2 Step 2: Estimate Parameters Using
estiParamSingle - 3 Step 3: Perform Differential Methylation Analysis Using
dmSingle - 4 Step 4: Perform Differential Methylation Analysis Using
plotGene - 5 Step 1: Load Two-Group Data
- 6 Step 2: Estimate Parameters Using
estiParamTwoGroups - 7 Step 3: Perform Differential Methylation Analysis for Two-Group Comparison Using
dmTwoGroups - Session info
0.1 Introduction
mist (Methylation Inference for Single-cell along Trajectory) is an R package for differential methylation (DM) analysis of single-cell DNA methylation (scDNAm) data. The package employs a Bayesian approach to model methylation changes along pseudotime and estimates developmental-stage-specific biological variations. It supports both single-group and two-group analyses, enabling users to identify genomic features exhibiting temporal changes in methylation levels or different methylation patterns between groups.
This vignette demonstrates how to use mist for:
1. Single-group analysis.
2. Two-group analysis.
0.2 Installation
To install the latest version of mist, run the following commands:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
# Install mist from GitHub
BiocManager::install("https://github.com/dxd429/mist")From Bioconductor:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("mist")To view the package vignette in HTML format, run the following lines in R:
library(mist)
vignette("mist")0.3 Example Workflow for Single-Group Analysis
In this section, we will estimate parameters and perform differential methylation analysis using single-group data.
1 Step 1: Load Example Data
Here we load the example data from GSE121708.
library(mist)
library(SingleCellExperiment)
# Load sample scDNAm data
Dat_sce <- readRDS(system.file("extdata", "small_sampleData_sce.rds", package = "mist"))2 Step 2: Estimate Parameters Using estiParamSingle
# Estimate parameters for single-group
Dat_sce <- estiParamSingle(
Dat_sce = Dat_sce,
Dat_name = "Methy_level_group1",
ptime_name = "pseudotime"
)
# Check the output
head(rowData(Dat_sce)$mist_pars)## Beta_0 Beta_1 Beta_2 Beta_3 Beta_4
## ENSMUSG00000000001 1.270651 -0.47186806 0.32963522 0.30439744 0.06337645
## ENSMUSG00000000003 1.583218 1.01333604 4.92302942 -3.85246492 -2.44563463
## ENSMUSG00000000028 1.273106 -0.06555137 0.12842424 0.07653342 0.04178288
## ENSMUSG00000000037 1.036779 -3.76633385 9.86705756 -2.63385757 -3.50219738
## ENSMUSG00000000049 1.012547 -0.07209959 0.09435702 0.10397753 0.06180564
## Sigma2_1 Sigma2_2 Sigma2_3 Sigma2_4
## ENSMUSG00000000001 5.785907 13.672379 4.068507 1.737734
## ENSMUSG00000000003 23.993799 4.703801 5.297336 8.352908
## ENSMUSG00000000028 7.213110 10.411544 2.831234 2.389155
## ENSMUSG00000000037 9.043003 13.051445 7.157006 2.152556
## ENSMUSG00000000049 5.468817 9.001613 2.773162 1.3523813 Step 3: Perform Differential Methylation Analysis Using dmSingle
# Perform differential methylation analysis for the single-group
Dat_sce <- dmSingle(Dat_sce)
# View the top genomic features with drastic methylation changes
head(rowData(Dat_sce)$mist_int)## ENSMUSG00000000037 ENSMUSG00000000003 ENSMUSG00000000001 ENSMUSG00000000049
## 0.054961080 0.034931047 0.011385568 0.008574870
## ENSMUSG00000000028
## 0.0073298384 Step 4: Perform Differential Methylation Analysis Using plotGene
# Produce scatterplot with fitted curve of a specific gene
library(ggplot2)
plotGene(Dat_sce = Dat_sce,
Dat_name = "Methy_level_group1",
ptime_name = "pseudotime",
gene_name = "ENSMUSG00000000037")
4.1 Example Workflow for Two-Group Analysis
In this section, we will estimate parameters and perform DM analysis using data from two phenotypic groups.
5 Step 1: Load Two-Group Data
# Load two-group scDNAm data
Dat_sce <- readRDS(system.file("extdata", "small_sampleData_sce.rds", package = "mist"))6 Step 2: Estimate Parameters Using estiParamTwoGroups
# Estimate parameters for both groups
Dat_sce <- estiParamTwo(
Dat_sce = Dat_sce,
Dat_name_g1 = "Methy_level_group1",
Dat_name_g2 = "Methy_level_group2",
ptime_name_g1 = "pseudotime",
ptime_name_g2 = "pseudotime_g2"
)
# Check the output
head(rowData(Dat_sce)$mist_pars_group1, n = 3)## Beta_0 Beta_1 Beta_2 Beta_3 Beta_4
## ENSMUSG00000000001 1.265479 -0.84123852 0.6924136 0.45464430 -0.008571301
## ENSMUSG00000000003 1.599962 1.25715445 3.5920020 -2.47899071 -2.702329226
## ENSMUSG00000000028 1.287191 -0.05364528 0.1775574 0.05829547 -0.034220081
## Sigma2_1 Sigma2_2 Sigma2_3 Sigma2_4
## ENSMUSG00000000001 5.742699 14.095392 3.310469 1.949700
## ENSMUSG00000000003 23.957363 3.101447 5.547107 8.452306
## ENSMUSG00000000028 7.771315 7.754786 3.264941 2.367027head(rowData(Dat_sce)$mist_pars_group2, n = 3)## Beta_0 Beta_1 Beta_2 Beta_3 Beta_4
## ENSMUSG00000000001 1.9307436 -0.07123563 2.768290 -1.278696 -1.584433
## ENSMUSG00000000003 -0.7969592 -1.82910478 5.018215 -1.822206 -1.344583
## ENSMUSG00000000028 2.3177447 -1.45123158 6.183050 -5.731032 1.097013
## Sigma2_1 Sigma2_2 Sigma2_3 Sigma2_4
## ENSMUSG00000000001 5.859393 6.559744 3.477407 1.431118
## ENSMUSG00000000003 6.832205 8.706746 4.029906 2.716183
## ENSMUSG00000000028 11.170286 5.897188 3.501913 3.4148287 Step 3: Perform Differential Methylation Analysis for Two-Group Comparison Using dmTwoGroups
# Perform DM analysis to compare the two groups
Dat_sce <- dmTwoGroups(Dat_sce)
# View the top genomic features with different temporal patterns between groups
head(rowData(Dat_sce)$mist_int_2group)## ENSMUSG00000000037 ENSMUSG00000000003 ENSMUSG00000000001 ENSMUSG00000000049
## 0.03572091 0.03302410 0.02649985 0.01001201
## ENSMUSG00000000028
## 0.006968697.1 Conclusion
mist provides a comprehensive suite of tools for analyzing scDNAm data along pseudotime, whether you are working with a single group or comparing two phenotypic groups. With the combination of Bayesian modeling and differential methylation analysis, mist is a powerful tool for identifying significant genomic features in scDNAm data.
Session info
## R Under development (unstable) (2024-10-21 r87258)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] ggplot2_3.5.1 SingleCellExperiment_1.29.1
## [3] SummarizedExperiment_1.37.0 Biobase_2.67.0
## [5] GenomicRanges_1.59.1 GenomeInfoDb_1.43.2
## [7] IRanges_2.41.2 S4Vectors_0.45.2
## [9] BiocGenerics_0.53.3 generics_0.1.3
## [11] MatrixGenerics_1.19.0 matrixStats_1.4.1
## [13] mist_0.99.10 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.1 farver_2.1.2 dplyr_1.1.4
## [4] Biostrings_2.75.3 bitops_1.0-9 fastmap_1.2.0
## [7] RCurl_1.98-1.16 GenomicAlignments_1.43.0 XML_3.99-0.18
## [10] digest_0.6.37 lifecycle_1.0.4 survival_3.8-3
## [13] magrittr_2.0.3 compiler_4.5.0 rlang_1.1.4
## [16] sass_0.4.9 tools_4.5.0 yaml_2.3.10
## [19] rtracklayer_1.67.0 knitr_1.49 labeling_0.4.3
## [22] S4Arrays_1.7.1 curl_6.1.0 DelayedArray_0.33.3
## [25] abind_1.4-8 BiocParallel_1.41.0 withr_3.0.2
## [28] grid_4.5.0 colorspace_2.1-1 scales_1.3.0
## [31] MASS_7.3-63 mcmc_0.9-8 tinytex_0.54
## [34] cli_3.6.3 mvtnorm_1.3-2 rmarkdown_2.29
## [37] crayon_1.5.3 httr_1.4.7 rjson_0.2.23
## [40] cachem_1.1.0 zlibbioc_1.53.0 splines_4.5.0
## [43] parallel_4.5.0 BiocManager_1.30.25 XVector_0.47.1
## [46] restfulr_0.0.15 vctrs_0.6.5 Matrix_1.7-1
## [49] jsonlite_1.8.9 SparseM_1.84-2 carData_3.0-5
## [52] bookdown_0.41 car_3.1-3 MCMCpack_1.7-1
## [55] Formula_1.2-5 magick_2.8.5 jquerylib_0.1.4
## [58] snow_0.4-4 glue_1.8.0 codetools_0.2-20
## [61] gtable_0.3.6 BiocIO_1.17.1 UCSC.utils_1.3.0
## [64] munsell_0.5.1 tibble_3.2.1 pillar_1.10.1
## [67] htmltools_0.5.8.1 quantreg_5.99.1 GenomeInfoDbData_1.2.13
## [70] R6_2.5.1 evaluate_1.0.1 lattice_0.22-6
## [73] Rsamtools_2.23.1 bslib_0.8.0 MatrixModels_0.5-3
## [76] Rcpp_1.0.13-1 coda_0.19-4.1 SparseArray_1.7.2
## [79] xfun_0.50 pkgconfig_2.0.3