pedFlagHomo {fbat} | R Documentation |
Flag homo/heterozygotes.
pedFlagHomo(geneSetObj, founderOnly=TRUE, quiet=FALSE) pedFlagHomo.default(pedObj, founderOnly=TRUE, quiet=FALSE)
geneSetObj |
a geneSet object. |
pedObj |
a list with five elements: ped , columns , markerNames , Position , and filename . ped is a 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 are the 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; markerNames is a vector of marker names; Position is a vector of marker positions; fileName is the pedigree file name |
founderOnly |
indicates if using only founder info |
quiet |
print intermediate results if quiet=FALSE . |
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. |
Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus ross.lazarus@channing.harvard.edu, Gregory Warnes warnes@bst.rochester.edu, Nitin Jain nitin.jain@pfizer.com
data(CAMP) res<-pedFlagHomo(CAMP) res$countMat res$flagHomoMat res$markerNames