write_control_file: Write a control file for QTL data
In simecek/qtl2: Tools for analyzing high-dimensional QTL experiments

Description Usage Arguments Details Value See Also Examples

Write the control file (in YAML needed by read_cross2 for a set of QTL data.

write_control_file(output_file, crosstype, geno_file, foundergeno_file,
  gmap_file, pmap_file, pheno_file, covar_file, phenocovar_file, sex_file,
  sex_covar, sex_codes, crossinfo_file, crossinfo_covar, crossinfo_codes,
  linemap_file, linemap_covar, geno_codes, alleles, xchr, na.strings = c("-",
  "NA"), comments)

`output_file`	File name (with path) of the YAML file to be created, as a character string.
`crosstype`	Character string with the cross type.
`geno_file`	File name for genotype data.
`foundergeno_file`	File name for the founder genotype data.
`gmap_file`	File name for genetic map.
`pmap_file`	File name for the physical map.
`pheno_file`	File name for the phenotype data.
`covar_file`	File name for the covariate data.
`phenocovar_file`	File name for the phenotype covariate data (i.e., metadata about the phenotypes).
`sex_file`	File name for the individuals' sex. (Specify just one of `sex_file` or `sex_covar`.)
`sex_covar`	Column name in the covariate data that corresponds to sex. (Specify just one of `sex_file` or `sex_covar`.)
`sex_codes`	Named vector of character strings specifying the encoding of sex. The names attribute should be the codes used in the data files; the values within the vector should be `"female"` and `"male"`.
`crossinfo_file`	File name for the `cross_info` data. (Specify just one of `crossinfo_file` or `crossinfo_covar`.)
`crossinfo_covar`	Column name in the covariate data that corresponds to the `cross_info` data. (Specify just one of `crossinfo_file` or `crossinfo_covar`.)
`crossinfo_codes`	In the case that `crossinfo_covar` is provided (and not `crossinfo_file`; it would be left untouched), a named vector of character strings specifying the encoding of `cross_info`. The names attribute should be the codes used in the covariate column; the values within the vector should be the codes to which they will be converted (for example, `0` and `1` for an intercross).
`linemap_file`	File name for the `linemap` data (indicating the mapping of individuals to lines). (Specify just one of `linemap_file` or `linemap_covar`.)
`linemap_covar`	Column name in the covariate data that corresponds to the `linemap` data. (Specify just one of `linemap_file` or `linemap_covar`.)
`geno_codes`	Named vector specifying the encoding of genotypes. The names attribute has the codes used within the genotype and founder genotype data files; the values within the vector should be the integers to which the genotypes will be converted.
`alleles`	Vector of single-character codes for the founder alleles.
`xchr`	Character string with the ID for the X chromosome.
`na.strings`	Vector of character strings with codes to be treated as missing values.
`comments`	Vector of character strings to be inserted as comments at the top of the file, with each string as a line.

This function takes a set of parameters and creates the control file (in YAML format) needed for the new input data file format for R/qtl2. See the sample data files and the vignette describing the input file format.

(Invisibly) The data structure that was written.

read_cross2, sample data files at http://kbroman.org/qtl2/pages/sampledata.html

## Not run: 
# Control file for the sample dataset, grav2
write_control_file("~/my_data/grav2.yaml",
                   crosstype="riself",
                   geno_file="grav2_geno.csv",
                   gmap_file="grav2_gmap.csv",
                   pheno_file="grav2_pheno.csv",
                   phenocovar_file="grav2_phenocovar.csv",
                   geno_codes=c(L=1L, C=2L),
                   alleles=c("L", "C"),
                   na.strings=c("-", "NA"))

# Control file for the sample dataset, iron
write_control_file("~/my_data/iron.yaml",
                   crosstype="f2",
                   geno_file="iron_geno.csv",
                   gmap_file="iron_gmap.csv",
                   pheno_file="iron_pheno.csv",
                   covar_file="iron_covar.csv",
                   phenocovar_file="iron_phenocovar.csv",
                   geno_codes=c(SS=1L, SB=2L, BB=3L),
                   sex_covar="sex",
                   sex_codes=c(f="female", m="male"),
                   crossinfo_covar="cross_direction",
                   crossinfo_codes=c("(SxB)x(SxB)"=0L, "(BxS)x(BxS)"=1L),
                   xchr="X",
                   alleles=c("S", "B"),
                   na.strings=c("-", "NA"))

## End(Not run)