mendelian_check: 'Create GBS.array objects'

In yangjl/imputeR: Imputation of GBS genotypes via window phasing

Description

Create GBS.array objects from Geno4imputeR objects. It will compute population allele frq based on families of selfed kids. Original Geno4imputeR will be updated and returned. A set of GBS.array objects will be output to the directory by chromosomes.

Usage

mendelian_check(geno, ped, self_cutoff, depth_cutoff)

subcheck(subgeno, depth_cutoff)

Arguments

ped	a data.frame of pedigree information, must include three columns: proid (progeny id), parent1 (the first parent id), parent2 (the 2nd parent id).
Geno4imputeR	input object.
outdir	path of the output dir.
maf_cutoff	cutoff for MAF, default=0.002.
lmiss_cutoff	cutoff for locus missing rate, default=0.8.
imiss_cutoff	cutoff for individual missing rate, default=0.8.
size_cutoff	Minimum family size required for imputation, default=40.

Value

Return updated Geno4imputeR object. The GBS.array objects will be output to the given directory by family and chr.

Details of the GBS.array objects. Slot1: true_parents, a list of data.frame(hap1, hap2). Slot2: gbs_parents, a list of genotypes. For example, c(1, 2, 2, 0, 3). Slot3: true_kids, a list of data.frame(hap1, hap2). Slot4: gbs_kids, a list of kid genotypes. For example, c(1, 1, 3, 1, 2). Slot5: pedigree, a data.frame (kid, p1, p2). Note, p1 is the focal parent. Slot6: freq, a vector of reference allele freq for all SNPs.

See https://github.com/yangjl/imputeR/blob/master/vignettes/imputeR-vignette.pdf for more details.

Examples

create_array(Geno4imputeR, ped, outdir="largedata/", 
maf_cutoff=0.002, lmiss_cutoff=0.8, imiss_cutoff=0.8, size_cutoff=40)

yangjl/imputeR documentation built on May 4, 2019, 2:28 p.m.