pedFlagHomo {fbat} | R Documentation |
flag homo/heterozygotes
Description
Flag homo/heterozygotes.
Usage
pedFlagHomo(geneSetObj, founderOnly=TRUE, quiet=FALSE)
pedFlagHomo.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 family (pedigree id), pid (patient id), father (father id), mother (mother id), sex, affected (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","affected") or equal to c("family","pid","father","mother","sex") |
founderOnly |
indicates if using only founder info |
quiet |
print intermediate results if quiet=FALSE . |
Value
countMat |
Count the number of homo/heterozygotes. |
flagHomoMat |
Flag homo/heterozygotes. 1 – homozygotes; 0 – heterozygotes; -1 – genotype contains one missing allele; -2 – genotype contains two missing alleles. |
markerNames |
marker names. |
Author(s)
Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus ross.lazarus@channing.harvard.edu
Examples
data(CAMP)
res<-pedFlagHomo(CAMP)
res$countMat
res$flagHomoMat
res$markerNames
[Package
fbat version 1.0.0
Index]