batchCallGeno: Genotyping all sample by chromsome

In binmapr: Call Marker from Snp Data using Binmap

Description

The genotype of each sample will be called according to their allele depth, and then the potential error will be fixed.

Usage

batchCallGeno(x, CHROM, outdir = ".", window.size = 15,
  low.count = 6, high.count = 24, fix.size = 5, pos.start = 6,
  pdf.height = 4, pdf.width = 8)

Arguments

x	GT matrix
CHROM	chromosome vector
outdir	outdir
window.size	parameter of callWindowGeno
low.count	parameter of callWindowGeno
high.count	parameter of callWindowGeno
fix.size	parameter of fixGenoError
pos.start	position start index, for exmaple, the pos.start of chr1_1234 is 6, chr01_1234 is 7
pdf.height	pdf width
pdf.width	pdf width

Value

A list object including genotype of each chromosome. It will also create PDF and CSV of these genotype.

Author(s)

Zhougeng xu

Examples

data(geno) 
GT <- as.matrix(geno[1:100,5:6])
row.names(GT) <- paste0(geno$CHR[1:100], "_", geno$POS[1:100])
temp_dir <- tempdir()
gt <- batchCallGeno(GT, "chr01",  outdir = temp_dir, pos.start = 7)

binmapr documentation built on Oct. 30, 2019, 12:14 p.m.