mendelErr {SeqVarTools} | R Documentation |
Detect Mendelian errors
## S4 method for signature 'SeqVarGDSClass' mendelErr(gdsobj, pedigree, use.names=FALSE, autosomes=1:22, xchrom="X", ychrom="Y", verbose=TRUE)
gdsobj |
A |
pedigree |
A data.frame with columns (family, individ, father,
mother, sex, sample.id). "sex" column should have values "M"/"F".
"sample.id" values should correspond to "sample.id" in |
use.names |
A logical indicating whether to assign variant IDs as names of the output vector. |
autosomes |
A vector with chromosome values in |
xchrom |
The chromosome value in |
ychrom |
The chromosome value in |
verbose |
A logical indicating whether to print the number of samples selected for each trio. |
Mendelian errors are detected for each trio in pedigree
. Duos
(mother or father missing) are included. The pedigree must have only
one sample per individual.
A list with the following elements:
by.variant |
An integer vector with the number of mendelian errors detected for
each variant. If |
by.trio |
An integer vector with the number of mendelian errors detected for each trio. The vector will be named with the sample ID of the child in each trio. |
Stephanie Gogarten
gds <- seqOpen(seqExampleFileName("gds")) data(pedigree) err <- mendelErr(gds, pedigree) table(err$by.variant) err$by.trio seqClose(gds)