shmootl: QTL Analysis Utilities for Yeast

Description Usage Arguments Details See Also

Recode data in an R/qtl cross or genotype CSV file. Genotypes can be recoded by passing to the geno parameter a mapping of old to new genotypes. Alternatively, genotype data can be converted to enumerated genotypes with the enum.geno parameter.

1	run_recode(datafile = NA_character_, geno = mapping(), enum.geno = FALSE)

`datafile`	cross/geno CSV file [required]
`geno`	recode genotypes from mapping
`enum.geno`	recode to enumerated genotypes

When calling this function from within the R environment, the geno parameter must be specified as a mapping object (e.g. mapping( c(A = 'W', B = 'S') )). When called from the command line using Rscript, the geno parameter must be specified as a a YAML string (or YAML file) mapping old to new genotypes (e.g. "A: W, B: S").

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