cisAssoc: test for variant-expression associations in cis, using VCF
In GGtools: software and data for analyses in genetics of gene expression

Description Usage Arguments Details Value Note Author(s) Examples

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

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

`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

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.

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

seqlevelsStyle for summex and vcf.tf content must agree

VJ Carey <stvjd@channing.harvard.edu>

 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)]