subsetChromosome: Subset genotypeR object by chromosome

In genotypeR: SNP Genotype Marker Design and Analysis

Description

subsetChromosome subsets a genotypeR object based on the supplied chromosome name (must be the same as that in the data).

Usage

subsetChromosome(aa, chromosome)

Arguments

aa	genotypeR object before binary coding
chromosome	which chromosome to pull out (e.g., "chr2")

Value

A genotypeR object subset based on the pattern supplied with chromosome

Examples

data(genotypes_data)
data(markers)
## genotype table
marker_names <- make_marker_names(markers)
GT_table <- Ref_Alt_Table(marker_names)
## remove those markers that did not work
genotypes_data_filtered <- genotypes_data[,c(1, 2, grep("TRUE",
colnames(genotypes_data)%in%GT_table$marker_names))]

warnings_out2NA <- initialize_genotypeR_data(seq_data = genotypes_data_filtered,
genotype_table = GT_table, output = "warnings2NA")
chromosome_subset <- subsetChromosome(warnings_out2NA, "chr2")

genotypeR documentation built on May 2, 2019, 8:25 a.m.