Description Usage Arguments Value Examples
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.
1 |
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) |
genotypeR object with counted crossovers
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.