pedAFreq {fbat} | R Documentation |
get allele frequencies
Description
Get allele frequencies (missing alleles allowed).
Usage
pedAFreq(geneSetObj, founderOnly=TRUE, quiet=FALSE)
pedAFreq.default(ped,
columns=c("family","pid","father","mother","sex","affected"),
founderOnly=TRUE,
quiet=FALSE)
Arguments
geneSetObj |
a geneSet object. |
ped |
pedigree data frame whose first 6 columns are pid (pedigree id), id (individual id), fid (father id), mid (mother id), sex, aff (affection status). The remaining columns are pairs of marker alleles. Each row corresponds to an individual. |
columns |
names of the first 5 (or 6) columns of ped file. It should be either equal to c("family","pid","father","mother","sex","affect") or equal to c("family","pid","father","mother","sex") |
founderOnly |
indicates if using only founder info |
quiet |
print intermediate results if quiet=FALSE . |
Value
aFreqMat |
allele frequencies. |
aPercMat |
allele percentages. |
Author(s)
Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus ross.lazarus@channing.harvard.edu
Examples
data(CAMP)
res<-pedAFreq(CAMP)
res$aFreqMat
res$aPercMat
[Package
fbat version 1.0.0
Index]