HM2rac {GGtools} | R Documentation |
compute rare allele count from a hapmap file
HM2rac(fn, comment.char="", kppref="NA") thinHM2rac(gzfn) countRare(x) getRare(x)
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. |
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.
Vince Carey <stvjc@channing.harvard.edu>
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"))