read.mapmaker: Read data from a Mapmaker raw file

In bschiffthaler/BatchMap: Software for the Creation of High Density Linkage Maps in Outcrossing Species

Description

Imports data from a Mapmaker raw file.

Usage

read.mapmaker(dir, file)

Arguments

dir	directory where the input file is located.
file	the name of the input file which contains the data to be read.

Details

For details about MAPMAKER files see Lincoln et al. (1993). The current version supports backcross, F2s and RIL populations. The file can contain phenotypic data, but it will not be used in the analysis.

Value

An object of class onemap, i.e., a list with the following components:

geno	a matrix with integers indicating the genotypes read for each marker in onemap fashion. Each column contains data for a marker and each row represents an individual.
geno.mmk	a matrix with integers indicating the genotypes read for each marker in MAPMAKER/EXP fashion, i.e., 1, 2, 3: AA, AB, BB, respectively; 3, 4: BB, not BB, respectively; 1, 5: AA, not AA, respectively. Each column contains data for a marker and each row represents an individual.
n.ind	number of individuals.
n.mar	number of markers.
segr.type	a vector with the segregation type of each marker, as strings. Segregation types were adapted from outcross segregation types, using the same notation. For details see read.onemap.
segr.type.num	a vector with the segregation type of each marker, represented in a simplified manner as integers. Segregation types were adapted from outcross segregation types. For details see read.onemap.
input	the name of the input file.
n.phe	number of phenotypes.
pheno	a matrix with phenotypic values. Each column contains data for a trait and each row represents an individual. Currently ignored.

Author(s)

Adapted from Karl Broman (package qtl) by Marcelo Mollinari, [e-mail]

References

Broman, K. W., Wu, H., Churchill, G., Sen, S., Yandell, B. (2008) qtl: Tools for analyzing QTL experiments R package version 1.09-43

Lincoln, S. E., Daly, M. J. and Lander, E. S. (1993) Constructing genetic linkage maps with MAPMAKER/EXP Version 3.0: a tutorial and reference manual. A Whitehead Institute for Biomedical Research Technical Report.

Examples

  ## Not run: 
    map_data <-read.mapmaker(dir="work_directory",file="data_file.txt")
  
## End(Not run)

bschiffthaler/BatchMap documentation built on Dec. 16, 2019, 2:22 a.m.