create_array: '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

create_array(geno, ped, pargeno, pp = NULL, pinfo = NULL,
  outdir = "largedata/obs", bychr = FALSE, bychunk = NULL)

get_snpinfo(geno, ped, self_cutoff)

pedinfo(ped)

est_pop_maf(geno, pinfo, ped, self_cutoff)

est_maf(pgeno)

est_missing(pgeno)

ped_focal(ped, pargeno, focalp)

get_array_item(subgeno, myped, focalp, pp)

Arguments

geno	a data.frame of gentoype. coded with 0 (major), 1 (het), 2 (minor) and 3 (missing).
ped	a data.frame of pedigree information, must include three columns: proid (progeny id), parent1 (the first parent id), parent2 (the 2nd parent id).
pargeno	A data.frame with two columns: "parentid" and "true_p". The 2nd column indicates whether the true parental genotype is available.
outdir	path of the output dir.
bychr	Wether to split the data by 10 chromsomes.

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.