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.
Returns
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
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.
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.
Author(s)
Adapted from Karl Broman (package qtl) by Marcelo Mollinari, mmollina@usp.br