Description Usage Arguments Value Examples
subsetChromosome
subsets a genotypeR object based on
the supplied chromosome name (must be the same as that in the data).
1 | subsetChromosome(aa, chromosome)
|
aa |
genotypeR object before binary coding |
chromosome |
which chromosome to pull out (e.g., "chr2") |
A genotypeR object subset based on the pattern supplied with chromosome
1 2 3 4 5 6 7 8 9 10 11 12 | 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")
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