riskyAlleleCount: given a matrix of subjects x SNP calls, count number of risky...

In vjcitn/gwascat: representing and modeling data in the EMBL-EBI GWAS catalog

Description

given a matrix of subjects x SNP calls, count number of risky alleles for various conditions, relative to NHGRI GWAS catalog

Usage

riskyAlleleCount(callmat, matIsAB = TRUE, chr, 
  gwwl , snpap = "SNPlocs.Hsapiens.dbSNP144.GRCh37",
  gencode = c("A/A", "A/B", "B/B"))

Arguments

callmat	matrix with subjects as rows, SNPs as columns; entries can be generic A/A, A/B, B/B, or specific nucleotide calls
matIsAB	logical, FALSE if nucleotide codes are present, TRUE if generic call codes are present; in the latter case, gwascat:::ABmat2nuc will be run
chr	code for chromosome, should work with the SNP annotation getSNPlocs function, so likely "ch[nn]"
gwwl	an instance of gwaswloc
snpap	name of a Bioconductor SNPlocs.Hsapiens.dbSNP.* package
gencode	codes used for generic SNP call

Value

matrix with rows corresponding to subjects , columns corresponding to SNP

Examples

data(gg17N) # translated from GGdata chr 17 calls using ABmat2nuc
data(ebicat37)
library(GenomeInfoDb)
seqlevelsStyle(ebicat37) = "UCSC"
h17 = riskyAlleleCount(gg17N, matIsAB=FALSE, chr="ch17", gwwl=ebicat37)
h17[1:5,1:5]
table(as.numeric(h17))

vjcitn/gwascat documentation built on May 5, 2019, 7:59 p.m.