read_data: Read data files

In jendelman/diaQTL: QTL Analysis in Diallel Populations

Read data files

Description

Reads genotype, pedigree, and phenotype data files

Usage

read_data(
  genofile,
  ploidy = 4,
  pedfile,
  phenofile = NULL,
  fixed = NULL,
  bin.markers = TRUE,
  dominance = NULL,
  n.core = 1
)

Arguments

genofile	File with map and genotype probabilities
ploidy	Either 2 or 4
pedfile	File with pedigree data (id,parent1,parent2)
phenofile	File with phenotype data (optional)
fixed	If there are fixed effects, this is a character vector of "factor" or "numeric"
bin.markers	TRUE/FALSE whether to bin markers with the same cM position
dominance	Maximum value of dominance that will be used for analysis. Default = ploidy.
n.core	Number of cores for parallel execution

Details

The first 3 columns of the genotype file should be the genetic map (labeled marker, chrom, cM), and a fourth column for a reference genome position (labeled bp) can also be included. The map is followed by the members of the population. The genotype data for each marker x individual combination is a string with the format "state|state|state...=>prob|prob|prob...", where "state" refers to the genotype state and "prob" is the genotype probability in decimal format. Only states with nonzero probabilities need to be listed. The encoding for the states in tetraploids is described in the documentation for the F1codes and S1codes datasets that come with the package. For diploids, there are 4 F1 genotype codes, 1,2,3,4, which correspond to haplotype combinations 1-3,1-4,2-3,2-4, respectively; the S1 genotype codes 1,2,3 correspond to 1-1,1-2,2-2, respectively.

For the phenotype file, first column is id, followed by traits, and then any fixed effects. Pass a character vector for the function argument "fixed" to specify whether each effect is a factor or numeric covariate. The number of traits is deduced based on the number of columns. Binary traits must be coded N/Y and are converted to 0/1 internally for analysis by probit regression. Missing data in the phenotype file should be coded as NA.

The parameter dominance specifies the maximum value of dominance that can be used in subsequent analysis: 1 = additive, 2 = digenic dominance, 3 = trigenic dominance, 4 = quadrigenic dominance. The default is dominance = ploidy, which allows the full range of dominance models in functions such as scan1 and fitQTL, but this requires the most RAM. Output files from the BGLR package are stored in a folder named 'tmp' in the current directory.

Value

Variable of class diallel_geno if phenofile is NULL, otherwise diallel_geno_pheno

Examples

## Not run: 
  ## Get the location of raw csv files examples
  genocsv = system.file( "vignette_data", "potato_geno.csv", package = "diaQTL" )
  pedcsv = system.file( "vignette_data", "potato_ped.csv", package = "diaQTL" )
  phenocsv = system.file( "vignette_data", "potato_pheno.csv", package = "diaQTL" )
  
  ## Check their location in the system
  print(genocsv)
  print(pedcsv)
  print(phenocsv)
  
  ## Load them in R
  diallel_example <- read_data(genofile = genocsv,
                               ploidy = 4,
                               pedfile = pedcsv,
                               phenofile = phenocsv)

## End(Not run)

jendelman/diaQTL documentation built on Jan. 27, 2024, 6:39 a.m.