gQTLs {gQTLstats} | R Documentation

## use SummarizedExperiment to manage a collection of gQTL results of interest

### Description

use SummarizedExperiment to manage a collection of gQTL results of interest

### Usage

    gQTLs(filtgr, se, tf, genome = "hg19", forceRs = TRUE, chunksize = 50)
    gQTLswarm(se, ind, covar = NULL, inpch = 19, xlab, ylab, featTag="probeid", ...)

### Arguments

`filtgr` | a GRanges instance typically obtained by filtering a ciseStore instance
`se` | SummarizedExperiment with individual level expression and sample-level data from which filtgr statistics were derived; for gQTLswarm, output of gQTLs
`tf` | TabixFile for VCF on which filtgr statistics are based
`genome` | tag for `readVcf`
`forceRs` | if TRUE insist that snp ids include 'rs'
`chunksize` | VCF processing proceeds via foreach in chunks of size chunksize
`ind` | index into rows of se to be used for visualization, must be length 1
`covar` | a character string indicating a variable in colData(se) to be used to color the points
`inpch` | pch setting for dots in swarm
`xlab` | xlabel for beeswarm plot, defaults to snp id as recovered from rowRanges(se)$snp
`ylab` | ylabel for beeswarm plot, defaults to probe id as recovered from rowRanges(se)$probeid
`featTag` | element of mcols(rowRanges(se)) used to find ylab text, defaults to 'probeid', 'symbol' is often preferred
`...` | passed to `beeswarm`

### Value

a SummarizedExperiment instance with two assays, the first is genotype the second is expression

### Note

very preliminary

### Examples

    require(Rsamtools)
    tf = TabixFile(system.file("vcf/litv.vcf.gz", package="gQTLstats"))
    data(sigInlit) # 33 loci with significant cis eQTL on a specific filtering
    library(geuvPack)
    data(geuFPKM)
    require(doParallel)
    registerDoSEQ()
    gdem = gQTLs(sigInlit, geuFPKM, tf, genome = "hg19")
    gQTLswarm(gdem, 1, "popcode")

[Package gQTLstats version 1.12.0 Index]