cisAssoc {GGtools} | R Documentation

## 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

### 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.

### Value

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

### Note

seqlevelsStyle for summex and vcf.tf content must agree

### Author(s)

VJ Carey <stvjd@channing.harvard.edu>

### 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)]

[Package GGtools version 5.25.3 Index]