checkMendelian {fbat} | R Documentation |
Check Mendelian errors.
checkMendelian(geneSetObj, quiet = TRUE) checkMendelian.default(pedObj, quiet=TRUE)
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 |
quiet |
print intermediate results if quiet=FALSE . |
check the following errors:
A list with following elements:
errorFlag |
errorFlag=1 indicates the occurence of errors; errorFlag=0 indicates no error. |
compatibleFlag |
compatibleFlag=0 indicates the occurence of non-compatibility; compatibleFlag=1 indicates compatibility. |
nMerrMarker |
A $nMarkers x 1$ vector records the numbers of families with non-compatible genotypes, where $nMarkers$ is the number of markers. |
nMerrFamily |
A $nFamily x 1$ vector records the numbers of markers with non-compatible genotypes, where $nFamily$ is the number of families. |
nErrFamilySample |
A $nFamily x 1$ vector records the numbers of times that father id is equal to subject id or mother id is equal to subject id in a family. |
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) checkMendelian(CAMP, quiet = TRUE)