View source: R/format_qtlmap_geno.R
format_qtlmap_geno | R Documentation |
Generate files for QTL mapping
format_qtlmap_geno( bed, par_a, par_b, rm_het = TRUE, rm_miss = TRUE, include_pars = TRUE, out_fmt = "rqtl" )
bed |
A binary ped (bed) object created with the package 'gaston', likely either using the functions gaston::read.bed.matrix() or gaston::read.vcf() |
par_a |
String identifying the column in the SNP matrix containing data for the first parent. |
par_b |
String identifying the column in the SNP matrix containing data for the second parent. |
rm_het |
Logical indicating whether to remove SNPs that are heterozygous in either parent. |
rm_miss |
Logical indicating whether to remove SNPs that are missing in either parent. |
include_pars |
Logical indicating whether to include the parents in the output data |
out_fmt |
String indicating the format of the output table - one of either "icimapping" or "rqtl" |
This function will always remove SNPs that are monomorphic between the two parents, SNPs with missing data in both parents, and SNPs with with missing data in one parent and a heterozygous call in the other. The user can optionally specify whether to remove SNPs with missing data for either parent, or heterozygous calls in either parent. If "rqtl" output format is selected, a table suitable for use as the genotypic portion of the separate, rotated (i.e. "csvsr") R/qtl input format is produced.
list with components
abh |
Dataframe in A/B/H format (see details) |
flipped |
Character vector consisting of IDs of SNPs with flipped alleles |
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