HM2rac {GGtools} | R Documentation

## compute rare allele count from a hapmap file

### Description

compute rare allele count from a hapmap file

### Usage

    HM2rac(fn, comment.char="", kppref="NA")
    thinHM2rac(gzfn)
    countRare(x)
    getRare(x)

### Arguments

`fn` | filename string identifying hapmap genotyping file
`gzfn` | filename string identifying gzipped hapmap genotyping file
`x` | string vector of simple genotype calls (e.g., "AA")
`comment.char` | string identifying comment character token for read.table, should not be sharp sign because hapmap will use this in the header line
`kppref` | a character token that must be present to identify a sample header column. I.e., if kppref is "NA" then a column with header tag NAnnnnn will be kept but a column with header chrom will be dropped.

### Value

HM2rac returns a list including elements raremat: named character matrix with one row per snp and one column per sample, with snps named by rs numbers
alleles: named vector showing existing alleles at snp
rarealleles: named vector identifying base of rare allele
anno: character string for annotation indirection
countRare and getRare are simple string processing functions
`thinHM2meta` will create a `snpMeta-class` structure from a HapMap gzipped genotyping file.

### Author(s)

Vince Carey <stvjc@channing.harvard.edu>

### Examples

    fi = system.file("fileDemos/geno20demo.txt.gz", package="GGtools")
    racstr =  thinHM2rac(fi)
    names(racstr)
    racstr$rarecount[1:5,1:7]
    racstr$rarebase[1:6]
    racstr$alleles[1:6]
    getRare(c("AA", "AG", "GG", "GG"))
    countRare(c("AA", "AG", "GG", "GG"))

[Package GGtools version 1.6.1 Index]