geno2cross: Format a genotype matrix to a R/qtl readable file

In jtlovell/qtlTools: Data Processing and Plotting in Association with R/qtl

Description

geno2cross Combine marker information and genotype data into a R/qtl "csv" file.

Usage

geno2cross(genomat, chr = NULL, pos = NULL, id = NULL,
  chrpos.sep = "_", crossfile = "cross.csv")

Arguments

genomat	A matrix of individual (row) * marker (col) genotype calls.
chr	A vector of chromosome IDs. If null, taken from the column names
pos	A vector of marker positions. Must be able to be coerced to numeric (does not contain letters / special characters). If null, taken from the column names .
id	Individual identifiers. If NULL, taken from row names of genomat.
chrpos.sep	If chr and pos are NULL, use this character to parse marker names into chromosome and position information. For example, if chrpos.sep = "_", a marker named 01_100000 would be parsed into chr = 01 pos = 100000.
crossfile	The name of the cross file to be written. Defaults to store in current working directory. Specify full path if you want to write to another location.

Details

More here

Value

Nothing - writes a file called cross.file

Examples

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jtlovell/qtlTools documentation built on May 20, 2019, 3:14 a.m.