Description Usage Arguments Value Examples
convert2qtl_table
will take a genotypeR object that
contains binary coded genotypes, and export this to a csv
file suitable for use with Rqtl.
1 2 | convert2qtl_table(genotypeR_object,
temp_cross_for_qtl = "temp_cross_for_qtl.csv", chromosome_vect = NULL)
|
genotypeR_object |
this is a genotypeR object that has had genotypes coded as binary with binary_coding |
temp_cross_for_qtl |
name of the output file that will be output into the working directory |
chromosome_vect |
this is a vector of marker chromosome the length of the markers |
table to disk for input into rqtl
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | 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)
convert2qtl_table(count_CO, paste(temp_cross_for_qtl=getwd(),
"test_temp_cross.csv", sep="/"),
chromosome_vect=rep("2", (length(colnames(binary_genotypes(count_CO)))-2)))
|
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