read_geno-character-method function

read genotype data from file to one of several available objects, which can be passed to a GWASdata object GWASdata.

## S4 method for signature 'character'
read_geno(
  file.path,
  save.path = NULL,
  sep = " ",
  header = TRUE,
  use.fread = TRUE,
  use.big = FALSE,
  row.names = FALSE,
  ...
)

Arguments

• file.path: character giving the path to the data file to be read
• save.path: character containing the path for the backingfile
• sep: character. A field delimeter. See read.big.matrix for details.
• header: logical. Does the data set contain column names?
• use.fread: logical. Should the dataset be read using the function fread fread from package data.table?
• use.big: logical. Should the dataset be read using the function read.big.matrix from package bigmemory?
• row.names: logical. Does the dataset include rownames?
• ...: further arguments to be passed to read_geno.

Details

If the data set contains rownames specified, set option has.row.names = TRUE.

Examples

## Not run:

path <- system.file("extdata", "geno.txt", package = "kangar00")
geno <- read_geno(path, save.path = getwd(), sep = " ", use.fread = FALSE, row.names = FALSE)
## End(Not run)