riskyAlleleCount {gwascat} | R Documentation

## given a matrix of subjects x SNP calls, count number of risky alleles

### 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))

[Package gwascat version 2.20.1 Index]