missingGenotypeBySnpSex {GWASTools} | R Documentation |
For all SNPs for each sex tabulates missing SNP counts, allele counts and heterozygous counts.
missingGenotypeBySnpSex(genoData, scan.exclude = NULL, verbose = TRUE)
genoData |
|
scan.exclude |
A vector containing the scan numbers of scans that are to be excluded from the total scan list. |
verbose |
Logical value specifying whether to show progress information. |
This function calculates the fraction of missing genotypes for males
and females for each SNP given in genoData
.
A "sex" variable must be present in the scan
annotation slot of genoData
.
This function returns a list with three components: "missing.counts," "scans.per.sex," and "missing.fraction."
missing.counts |
A matrix with one row per SNP and one column per sex containing the number of missing SNP counts for males and females, respectively. |
scans.per.sex |
A vector containing the number of males and females respectively. |
missing.fraction |
A vector containing the fraction of missing counts for each SNP, with females excluded for the Y chromosome. |
Cathy Laurie, Stephanie Gogarten
GenotypeData
, missingGenotypeByScanChrom
library(GWASdata) file <- system.file("extdata", "illumina_geno.gds", package="GWASdata") gds <- GdsGenotypeReader(file) # need scan annotation with sex data(illuminaScanADF) genoData <- GenotypeData(gds, scanAnnot=illuminaScanADF) missingRate <- missingGenotypeBySnpSex(genoData) close(genoData)