run_makegeno: Make genotype data from VCF.
In gact/shmootl: QTL Analysis Utilities for Yeast

Description Usage Arguments Details See Also

Read raw genotype data from the sample VCF file, encode the given genotype data as founder or enumerated genotypes, and write the encoded genotypes to an R/qtl genotype CSV file.

1 2	run_makegeno(datafile = NA_character_, genfile = NA_character_, fdrfile = NA_character_, alleles = mapping(), digits = NA_integer_)

`datafile`	sample VCF file [required]
`genfile`	output genotype CSV file [required]
`fdrfile`	optional founder VCF file
`alleles`	founder allele symbol mapping
`digits`	numeric precision [default: unrounded]

If no founder VCF file is specified, markers are assigned enumerated genotypes, so that each raw allele is converted to a number in the order in which it is first observed at a given marker (i.e. '1', '2', etc.).

If a founder VCF file is given, markers are assigned a genotype symbol consisting of alleles that each correspond to a specific founder.

If the alleles parameter is specified, this must be a mapping of founder sample IDs to allele symbols. If calling this function from within the R environment, this must be specified as a mapping object (e.g. mapping( c(DBVPG6044 = 'W', Y12 = 'S') )). When called from the command line using Rscript, the alleles parameter must be specified as a YAML string (or YAML file) mapping founders to allele symbols (e.g. "DBVPG6044: W, Y12: S"). If the alleles parameter is not specified, allele symbols are taken from the letters of the alphabet (i.e. 'A', 'B' etc.).

Other pipeline functions: run_annoqtl, run_digest, run_estimap, run_interptimes, run_makecross, run_prep, run_pullmap, run_pushmap, run_recode, run_report, run_scanone, run_scantwo