read_population {cape}

Reads in data in the R/qtl csv format

Description

This function reads in a data file in the r/qtl format It converts letter genotypes to numbers if required. It parses the data into a data object. if filename is left empty, the script will ask the use to choose a file. phenotypes can be specified with a vector of column numbers or character strings. For each phenotype specified with a name, the script will find its location.

Usage

read_population(
  filename = NULL,
  pheno_col = NULL,
  geno_col = NULL,
  id_col = NULL,
  delim = ",",
  na_strings = "-",
  check_chr_order = TRUE,
  verbose = TRUE
)

Arguments

filename

The name of the file to read in

pheno_col

Column numbers of desired traits. The default behavior is to read in all traits.

geno_col

Column numbers of desired markers. The default behavior is to read in all markers.

id_col

The column number of an ID column. This is helpful to specify if the individual IDs are strings. Strings are only allowed in the ID column. All other trait data must be numeric.

delim

column delimiter for the file, default is ","

na_strings

a character string indicating how NA values are specified, default is "-"

check_chr_order

boolean, default is TRUE

verbose

A logical value indicating whether to print progress and cross information to the screen. Defaults to TRUE.

Value

This function returns a cape object in a former cape format. It must be updated using cape2mpp

References

Broman et al. (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890 doi:10.1093/bioinformatics/btg112

Examples

## Not run: 
cape_obj <- read_population("cross.csv")
combined_obj <- cape2mpp(cape_obj)
data_obj <- combined_obj$data_obj
geno_obj <- combined_obj$geno_obj

## End(Not run)