read_mapmaker: Read data from a Mapmaker raw file

In onemap: Construction of Genetic Maps in Experimental Crosses

Read data from a Mapmaker raw file

Description

Imports data from a Mapmaker raw file.

Usage

read_mapmaker(file = NULL, dir = NULL, verbose = TRUE)

Arguments

file	the name of the input file which contains the data to be read.
dir	directory where the input file is located.
verbose	A logical, if TRUE it output progress status information.

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.

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.
error	matrix containing HMM emission probabilities

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.

See Also

mapmaker_example_bc and mapmaker_example_f2 raw files in the package source.

Examples

 map_data <-read_mapmaker(file=system.file("extdata/mapmaker_example_f2.raw", package = "onemap"))
 #Checking 'mapmaker_example_f2'
 data(mapmaker_example_f2)
 names(mapmaker_example_f2)

onemap documentation built on Nov. 26, 2022, 9:05 a.m.