Read data from a Mapmaker raw file

Description

Imports data from a Mapmaker raw file.

Usage

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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, F_2 and RIL populations. The file can contain phenotypic data, but it will not be used in the analysis.

Value

An object of class bc.onemap, f2.onemap, riself.onemap or risib.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 list containing the type of cross and 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.outcross.

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.outcross.

phase

a numeric vector containing the linkage phase information between markers, i.e., 1 for coupling and -1 for repulsion, which is trivial for backcrosses, F_2 and RILs.

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, mmollina@usp.br

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

fake.bc.onemap and fake.f2.onemap directory in the package source.

Examples

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  ## Not run: 
    map_data <-read.mapmaker(dir="work_directory",file="data_file.txt")
    #Checking 'fake.f2.onemap'
    data(fake.f2.onemap)
    names(fake.f2.onemap)
  
## End(Not run)

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