write_control_file: Write a control file for QTL data
In rqtl/qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

write_control_file

R Documentation

Write a control file for QTL data

Description

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

Usage

write_control_file(
  output_file,
  crosstype = NULL,
  geno_file = NULL,
  founder_geno_file = NULL,
  gmap_file = NULL,
  pmap_file = NULL,
  pheno_file = NULL,
  covar_file = NULL,
  phenocovar_file = NULL,
  sex_file = NULL,
  sex_covar = NULL,
  sex_codes = NULL,
  crossinfo_file = NULL,
  crossinfo_covar = NULL,
  crossinfo_codes = NULL,
  geno_codes = NULL,
  alleles = NULL,
  xchr = NULL,
  sep = ",",
  na.strings = c("-", "NA"),
  comment.char = "#",
  geno_transposed = FALSE,
  founder_geno_transposed = FALSE,
  pheno_transposed = FALSE,
  covar_transposed = FALSE,
  phenocovar_transposed = FALSE,
  description = NULL,
  comments = NULL,
  overwrite = FALSE
)

Arguments

`output_file`	File name (with path) of the YAML or JSON file to be created, as a character string. If extension is `.json`, JSON format is used; otherwise, YAML is used.
`crosstype`	Character string with the cross type.
`geno_file`	File name for genotype data.
`founder_geno_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 there is a single cross info column (whether in a file or as a covariate), you can provide a named vector of character strings specifying the encoding of `cross_info`. The names attribute should be the codes used; the values within the vector should be the codes to which they will be converted (for example, `0` and `1` for an intercross).
`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.
`sep`	Character string that separates columns in the data files.
`na.strings`	Vector of character strings with codes to be treated as missing values.
`comment.char`	Character string that is used as initial character in a set of leading comment lines in the data files.
`geno_transposed`	If TRUE, genotype file is transposed (with markers as rows).
`founder_geno_transposed`	If TRUE, founder genotype file is transposed (with markers as rows).
`pheno_transposed`	If TRUE, phenotype file is transposed (with phenotypes as rows).
`covar_transposed`	If TRUE, covariate file is transposed (with covariates as rows).
`phenocovar_transposed`	If TRUE, phenotype covariate file is transposed (with phenotype covariates as rows).
`description`	Optional character string describing the data.
`comments`	Vector of character strings to be inserted as comments at the top of the file (in the case of YAML), with each string as a line. For JSON, the comments are instead included within the control object.
`overwrite`	If TRUE, overwrite file if it exists. If FALSE (the default) and the file exists, stop with an error.

Details

This function takes a set of parameters and creates the control file (in YAML or JSON 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.

Value

(Invisibly) The data structure that was written.

Examples

# Control file for the sample dataset, grav2
grav2_control_file <- file.path(tempdir(), "grav2.yaml")
write_control_file(grav2_control_file,
                   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
iron_control_file <- file.path(tempdir(), "iron.yaml")
write_control_file(iron_control_file,
                   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"))

# Remove these files, to clean up temporary directory
unlink(c(grav2_control_file, iron_control_file))

rqtl/qtl2 documentation built on March 20, 2024, 6:35 p.m.