read.mapmaker {onemap} | R Documentation |
Imports data from a Mapmaker raw file.
read.mapmaker(dir, file)
dir |
directory where the input file is located. |
file |
the name of the input file which contains the data to be read. |
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.
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 |
geno.mmk |
a list containing the type of cross and a matrix with integers indicating the genotypes
read for each marker in |
n.ind |
number of individuals. |
n.mar |
number of markers. |
segr.type |
a vector with the segregation type of each marker, as
|
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. |
Adapted from Karl Broman (package qtl) by Marcelo Mollinari, mmollina@usp.br
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.
fake.bc.onemap
and fake.f2.onemap
directory in the package source.
## 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)