qtl2: read_pheno – R documentation

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read_pheno

Read phenotype data

Description

Read phenotype data from a CSV file (and, optionally, phenotype covariate data from a separate CSV file). The CSV files may be contained in zip files, separately or together.

Usage

read_pheno(
  file,
  phenocovarfile = NULL,
  sep = ",",
  na.strings = c("-", "NA"),
  comment.char = "#",
  transpose = FALSE,
  quiet = TRUE
)

Arguments

`file`	Character string with path to the phenotype data file (or a zip file containing both the phenotype and phenotype covariate files).
`phenocovarfile`	Character string with path to the phenotype covariate file. This can be a separate CSV or zip file; if a zip file, it must contain exactly one CSV file. Alternatively, if the `file` argument indicates a zip file that contains two files (phenotypes and phenotype covariates), then this `phenocovarfile` argument must indicate the base name for the phenotype covariate file.
`sep`	the field separator character
`na.strings`	a character vector of strings which are to be interpreted as `NA` values.
`comment.char`	A character vector of length one containing a single character to denote comments within the CSV files.
`transpose`	If TRUE, the phenotype data will be transposed. The phenotype covariate information is never transposed.
`quiet`	If `FALSE`, print progress messages.

Value

Either a matrix of phenotype data, or a list containing pheno (phenotype matrix) and phenocovar (phenotype covariate matrix).

Examples

## Not run: 
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/master/Gough/gough_pheno.csv")
phe <- read_pheno(file)

phecovfile <- paste0("https://raw.githubusercontent.com/rqtl/",
                     "qtl2data/master/Gough/gough_phenocovar.csv")
phe_list <- read_pheno(file, phecovfile)

## End(Not run)

qtl2

Quantitative Trait Locus Mapping in Experimental Crosses

v0.24

GPL-3

Authors

Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>), R Core Team [ctb]

Initial release

2020-12-16