build_cross2_dataset: build_cross2_dataset

In lpalomerol/systematicQTL: Pipeline to run sistematically QTL analysis

Description

Generates cross2 dataset from basic geno and phenotypes name. Geno file should combine genenotype values and mapping (see to_csvs_geno) and phenotypes table should be a matrix-type object (users in rows, phenotypes in columns). This function is the entry point to QtlWrapper object.

Usage

build_cross2_dataset(
  geno_filename,
  pheno_filename,
  covar_column_names,
  pheno_column_names,
  genotypes = c("A", "H", "B"),
  alleles = c("A", "B"),
  na.strings = c("-1", "discrepancy", "NA"),
  comment.char = "#",
  ...
)

Arguments

geno_filename	Path to csvs geno file
pheno_filename	Path to csv pheno file
covar_column_names	List of "phenotype" columns related to adjusting covariates.
pheno_column_names	List of "phenotype" columns realted to main variables to study.
genotypes	List of allowed genotype values of genotypes file
alleles	List of homozygote alleles included, should be a subset of genotypes variable
na.strings	List of strings associated to NA values
comment.char	List or string of allowed comment chars
...	Additional arguments passed to read.cross function

Value

This function returns an R/QTL Object of class "cross2". For details, see the R/QTL2 developer guide.

Examples

## Not run: 
  geno_data_matrix_filename = '/path/to/geno_file'
  geno_map_filename = '/path/to/geno_mapping_file'
  phenotype_filenam = '/path/to/phenotypes_file'

  genotypes_csvs  = to_csvs_geno(geno_map_filename, geno_data_matrix_filename)
  write_csvs_geno(genotypes_csvs, '/path_to_geno_csvs')

  chosen_genotypes    = c('A', 'H', 'B')
  chosen_alleles      = c('A','B')
  chosen_covars       = c('pheno_var1', 'pheno_var2', 'pheno_var3')
  chosen_phenotypes   = c('signature1', 'signature2', 'signature3')

  cross2 = systematicQTL::build_cross2_dataset(
    geno_filename = geno_filename,
    pheno_filename = pheno_filename,
    covar_column_names = chosen_covars,
    pheno_column_names = chosen_phenotypes,
    alleles = chosen_alleles
  )


## End(Not run)

lpalomerol/systematicQTL documentation built on June 13, 2020, 5:12 p.m.