ABHgenotypeR (version 1.0.1)

readABHgenotypes: Read in the output of the genosToABH plugin.

Description

Read in the output of the genosToABH plugin.

Usage

readABHgenotypes(pathToABH, nameA = "A", nameB = "B", readPos = TRUE)

Arguments

pathToABH

The path and filename of the input file.

nameA

Name of the parent represented by "A" in the input file.

nameB

Name of the parent represented by "B" in the input file.

readPos

Should the function attempt read the physical position of markers from the input ?

Value

A genotype list object which holds the information from the input file. This list is the fundamental datastructure used by the other functions in this package. See the vignette for what each item in the list is.

Details

The input files should be a .csv file holding genotypes as specified by the qtl package and its "csvs" format. All characters in the genotype matrix which are not either A,B or H will be set to N. If readPos = TRUE (default) marker names must conform to S1_123456 meaning 123456 bp on chromosome 1. If FALSE, pos is set to NULL and needs to be manually constructed as shown in the examples. Note that this might throw off some plotting function.

Examples

## Not run: genotypes <- readABHgenotypes("./genotypes.csv", "NB", "OL")

 ## Not run: otherGenotypes <- readABHgenotypes("./otherGenotypes.csv", readPos = FALSE)
 #arbitrary position to keep marker order intact
 ## Not run: therGenotypes$pos <- 1:length(otherGenotypes$marker_names)