GGtools (version 5.8.0)

cisAssoc: test for variant-expression associations in cis, using VCF

Description

test for variant-expression associations in cis, using VCF and SummarizedExperiment representations

Usage

cisAssoc(summex, vcf.tf, rhs = ~1,  nperm = 3, cisradius = 50000,  genome = "hg19", assayind = 1, lbmaf = 1e-06, dropUnivHet = TRUE, doEsts=FALSE)
data(lgeu) # obtains an example SummarizedExperiment

Arguments

summex

instance of SummarizedExperiment-class

vcf.tf

instance of TabixFile, referring to a tabix-indexed, bgzipped VCF file

rhs

formula `right hand side' for adjustments to be made as snp.rhs.tests is run on each expression vector

nperm

number of permutations to be used for plug-in FDR computation

cisradius

distance in bp around each gene body to be searched for SNP association

genome

tag suitable for use in GenomeInfoDb structures

assayind

index of assays(summex) to use for expression data retrieval

lbmaf

lower bound on MAF of SNP to use

dropUnivHet

logical, if TRUE, will check for columns of SnpMatrix instance that possess no values other than "NA" and "A/B". See http://www.biostars.org/p/117155/#117270

doEsts

logical, if TRUE, will run snp.rhs.estimates and report beta and standard error

Value

a GRanges-class instance with mcols including chisq, permScore...

Details

snp.rhs.tests is the workhorse for statistical modeling. VCF content is transformed to the byte-code (which allows for uncertain imputation) and used in fast testing.

Examples

 data(lgeu) # small excerpt from GEUVADIS FPKM
 tf20 = TabixFile(system.file("vcf/c20exch.vcf.gz", package="GGtools"))
 if (require(VariantAnnotation)) scanVcfHeader(tf20)
 lgeue = clipPCs(lgeu[,which(lgeu$popcode=="CEU")], 1:2)
 set.seed(4321)
 litc = cisAssoc(lgeue, tf20, nperm=2, lbmaf=.05, cisradius=50000)
 litc2 = cisAssoc(lgeue, tf20, nperm=2, lbmaf=.05, cisradius=50000, doEsts=TRUE)
 summary(litc$chisq)
 litc$pifdr = pifdr(litc$chisq, c(litc$permScore_1, litc$permScore_2))
 litc[which(litc$pifdr < .01)]