arbitrary.cut.missing: A function transform the averaged score in to genotypes based...

In yanjunzan/GBSA: Genotype imputation and QTL mapping with ultra low coverage sequencing in pedigree

Description

unlike function arbitrary.cut . This function is a 4 point cut, which means uncertain region are leaved as missing.

Usage

arbitrary.cut.missing(geno, upper.cut, lower.cut, missing.upper, missing.lower)

Arguments

geno	the genotype matrix returned from creatExact function
upper.cut	threshold for calling homozygous genotype
lower.cut	threshold for calling homozygous alternative genotype
lower.cut	threshold for calling homozygous alternative genotype
missing.upper	bins with a averaged score below upper.cut but above missing.upper will be marked as missing.
missing.lower	bins with a averaged score above lower.cut but below missing.lower will be marked as missing.

Details

Updating

Value

return a data.frame with each bin transformed to "A" for homozygous and "B" for alternative genotype, "H" for heterozygous, NA for uncertain region

Author(s)

Yanjun Zan, Thibaut Payen

References

Yanjun Zan, Thibaut Payen, Leif Andersson, Paul B. Siegel and <c3><96>rjan Carlborg;Whole-genome QTL mapping in experimental pedigrees from outbred founders utilizing low coverage individual based sequencing 2018

Examples

See the package tutorial

yanjunzan/GBSA documentation built on May 14, 2019, 4:05 a.m.