count_CO: Internal function to remove search and remove columns based...

In genotypeR: SNP Genotype Marker Design and Analysis

Description

count_CO counts crossovers from binary coded genotypes in a genotypeR object. This function assigns crossovers to the counted_crossovers slot in a genotypeR object.

Usage

count_CO(data, naive = FALSE)

Arguments

data	genotype data read in with read_in_sequenom_data
naive	this takes 2 values: 1) FALSE (default) will count COs distributed by marker distance, and 2) TRUE returns will count COs without regard to marker distance (i.e., at the final non-missing data point in a string of missing genotypes)

Value

genotypeR object with counted crossovers

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")
binary_coding_genotypes <- binary_coding(warnings_out2NA, genotype_table = GT_table)
chr2 <- subsetChromosome(binary_coding_genotypes, chromosome="chr2")
count_CO <- count_CO(chr2)

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