misinherits: Find non-Mendelian inheritances in family data
Description
For SNP data in families, this function locates all subjects whose
parents are in the dataset and tests each SNP for non-Mendelian
inheritances in these trios.
Usage
misinherits(ped, id, father, mother, data = sys.parent(), snp.data)
Arguments
father
Identifiers for subjects' fathers
mother
Identifiers for subjects' mothers
data
A data frame in which to evaluate the previous four arguments
snp.data
An object of class "SnpMatrix"
containing the SNP
genotypes to be tested
Value
A logical matrix. Rows are subjects with any non-Mendelian
inheritances and columns are SNPs with any non-Mendelian
inheritances. The body of the matrix details whether each subject has
non-Mendelian inheritance at each SNP. If a subject has no recorded
genotype for a specific SNP, the corresponding element of the output
matrix is set to NA.
Details
The first four arguments are usually derived from a "pedfile". If a
data frame is supplied for the data
argument, the first four
arguments will be evaluated in this frame. Otherwise they will be evaluated
in the calling environment. If the arguments are missing, they will be
assumed to be in their usual positions in the pedfile data frame
i.e. in columns one to four. If the pedfile data are obtained from
a dataframe, the row names of the data
and snp.data
files will be used to align the pedfile and SNP data. Otherwise, these
vectors will be assumed to be in the same order as the rows of
snp.data
.
Examples
Run this codedata(families)
misinherits(data=pedData, snp.data=genotypes)
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