runIBDKING: Function just wrap snpgdsIBDKING

In belleau/aicsPaper: Accurate Inference of Genetic Ancestry from Cancer Sequencing

Function just wrap snpgdsIBDKING

Description

TODO

Usage

runIBDKING(gds, sampleId = NULL, snp.id = NULL, maf = 0.05)

Arguments

gds	an object of class SNPRelate::SNPGDSFileClass, a SNP GDS file.
sampleId	a vector of character strings representing the samples to keep for the analysis. If NULL, all samples are used. Default: NULL.
snp.id	a vector of character strings representing the SNPs to keep for the analysis. If NULL, all SNPs are used. Default: NULL.
maf	a single numeric representing the threshold for the minor allele frequency. Only the SNPs with ">= maf" are retained. Default: 0.05.

Value

a list containing:

• sample.ida character string representing the sample ids used in the analysis

• snp.ida character string representing the SNP ids used in the analysis

• k0a numeric, the IBD coefficient, the probability of sharing zero IBD

• k1a numeric, the IBD coefficient, the probability of sharing one IBD

• IBS0a numeric, the proportion of SNPs with zero IBS

• kinshipa numeric, the proportion of SNPs with zero IBS, if the parameter kinship=TRUE

Author(s)

Pascal Belleau, Astrid Deschênes and Alexander Krasnitz

Examples

# TODO
gds <- "Demo GDS TODO"

belleau/aicsPaper documentation built on Aug. 4, 2022, 1:12 a.m.