onemap (version 3.0.0)

read_mapmaker: Read data from a Mapmaker raw file

Description

Imports data from a Mapmaker raw file.

Usage

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

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

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.

Author

Adapted from Karl Broman (package qtl) by Marcelo Mollinari,

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.

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

# \donttest{
 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)
# }