<!--
%\VignetteIndexEntry{gQTLBase infrastructure for eQTL archives}
%\VignetteEngine{knitr::rmarkdown}
%\VignettePackage{gQTLBase}
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---
title: "gQTLBase: infrastructure for storage and interrogation of eQTL, mQTL,
  	  dsQTL etc. archives"
author: "Vincent J. Carey, stvjc at channing.harvard.edu"
date: "January 2015"
output:
  BiocStyle::html_document:
    highlight: pygments
    number_sections: true
    theme: united
    toc: true
  BiocStyle::pdf_document:
    toc: true
    number_sections: true
---

```{r style, echo = FALSE, results = 'asis'}
BiocStyle::markdown()
```


# Introduction

It is well-recognized that cis-eQTL searches with
dense genotyping yields billions of test results.  While
many are consistent with no association, it is hard to draw
an objective threshold, and targeted analysis may reveal
signals of interest that do not deserve penalization for
genome-wide search.

We recently performed a comprehensive cis-eQTL search
with the GEUVADIS FPKM expression measures.  The
most prevalent transcript types in this 
dataset are

```{r lktt,echo=FALSE}
litt = structure(c(15280L, 4853L, 1450L, 1153L, 476L, 114L), .Dim = 6L, .Dimnames = structure(list(
    c("protein_coding", "pseudogene", "antisense", "lincRNA", 
    "processed_transcript", "IG_V_gene")), .Names = "")
)
litt
```
*cis*-associated variation in abundance of
these entities
was assessed using 20 million 1000 genomes genotypes with
radius 1 million bases around each transcribed region.  There are
185 million SNP-transcript pairs in this analysis.  This
package (`r Biocpkg("gQTLBase")`) aims to simplify interactive interrogation of
this resource.

## Brief view of how the tests were done

The following function takes as argument 'chunk' a list with elements
chr (character token for indexing chromosomes in
genotype data in VCF) and genes (vector of gene identifiers).
It implicitly uses a `TabixFile` reference to acquire genotypes
on the samples managed in the `r Biocexptpkg("geuvPack")` package.

```{r eval=FALSE}
gettests = function( chunk, useS3=FALSE ) {
  library(VariantAnnotation)
  snpsp = gtpath( chunk$chr, useS3=useS3)
  tf = TabixFile( snpsp )
  library(geuvPack)
  if (!exists("geuFPKM")) data(geuFPKM)
  clipped = clipPCs(regressOut(geuFPKM, ~popcode), 1:10)
  set.seed(54321)
  ans = cisAssoc( clipped[ chunk$genes, ], tf, cisradius=1000000, lbmaf=0.01 )
  metadata(ans)$prepString = "clipPCs(regressOut(geuFPKM, ~popcode), 1:10)"
  ans
  }
```

`cisAssoc` returns a `GRanges` instance with fields relevant to computing
FDR for cis association.

A `r CRANpkg("BatchJobs")` registry is created as follows:

```{r bjreg,eval=FALSE}
flatReg = makeRegistry("flatReg",  file.dir="flatStore",
        seed=123, packages=c("GenomicRanges",
            "GGtools", "VariantAnnotation", "Rsamtools",
            "geuvPack", "GenomeInfoDb"))
```

For any list 'flatlist' of pairs (chr, genes), the following
code asks the scheduler to run gettests on every element, when
it can.  Using the Channing cumulus cloud, the job ran on 40
hosts at a cost of 170 USD.
```{r dosub,eval=FALSE}
batchMap(flatReg, gettests, flatlist)
submitJobs(flatReg)
```

This creates a 'sharded' archive of 7GB of results managed by
a Registry object.


## Illustration on a subset

We have extracted 3 shards from the job for illustration with the
`r Biocpkg("gQTLBase")` package.
```{r getstuff,results="hide", echo=FALSE}
suppressPackageStartupMessages({
library(BiocGenerics)
library(Homo.sapiens)
library(stats4)
library(IRanges)
library(GGtools)
library(gQTLBase)
library(geuvStore)
options(BBmisc.ProgressBar.style="off")
})
```
```{r doone}
library(gQTLBase)
library(geuvStore)
mm = partialRegistry()
mm
```

`mm` here denotes a BatchJobs `Registry`.  We want to wrap
it lightly, adding maps from probes and addresses
of SNPs to job identifiers where these probes and SNPs
have been analyzed.
```{r wrap, cache=TRUE}
mm = ciseStore(mm, validJobs=partialIds(),
        addProbeMap = TRUE, addRangeMap = TRUE)
mm
```

There are various approaches available to get results
out of the store.  At present we don't want a full
API for result-level operations, so work from BatchJobs
directly:
```{r getr}
loadResult(mm@reg, 1)[1:3]
```


On a multicore machine or cluster, we can visit job results in parallel.
The `storeApply` function uses `r CRANpkg("BatchJobs")` `reduceResultsList` to transform
job results by a user-supplied function.  The reduction events
occur in parallel through `r Biocpkg("BiocParallel")` `bplapply` over a set
of job id chunks whose character can be controlled through
the `n.chunks` parameter.

We'll illustrate by taking the length of each result.
```{r setuplen}
library(BiocParallel)
library(parallel)
mp = MulticoreParam(workers=max(c(1, detectCores()-4)))
register(mp)
```
```{r getlen, cache=TRUE}
lens = storeApply(mm, length)
summary(unlist(lens))
```

It is possible to limit the scope of application by setting the
`ids` parameter in `storeApply`.

## Interrogating by probe

For a known GEUVADIS Ensembl identifier (or vector
thereof) we can acquire all cis association test results as follows.

```{r doex,cache=TRUE}
pvec = mm@probemap[1:4,1]  # don't want API for map, just getting examples
litex = extractByProbes( mm, pvec )
length(litex)
litex[1:3]
```

We also have extractByRanges.

# Towards estimation of distributions relevant to FDR computation 

## Small-footprint collection of association statistics

In the gQTLstats package,
we will use the plug-in FDR algorithm of Hastie, Tibshirani and
Friedman *Elements of Statistical Learning* ch. 18.7, algorithm
18.3.  We will not handle hundreds of millions of scores directly
in a holistic way, except for the estimation of quantiles of the observed
association scores.  This particular step is carried out 
using `r CRANpkg("ff")` and
`r CRANpkg("ffbase")` packages.  We illustrate with our subset of GEUVADIS scores.


```{r getfff}
allassoc = storeToFf(mm, "chisq")
length(allassoc)
object.size(allassoc)
allassoc[1:4]
```

## Other statistical functions

Refer to the `r Biocpkg("gQTLstats")` package for additional
functions that generate quantile estimates, histograms, and
FDR estimates based on `ciseStore` contents and various
filtrations thereof.
