Imports data from a full-sib family derived from the cross of two
outbred parents and creates an object of class outcross.
read.outcross(dir, file)directory where the input file is located.
the name of the input file which contains the data to be read.
An object of class outcross, i.e., a list with the following
components:
a matrix with integers indicating the genotypes read for each marker. Each column contains data for a marker and each row represents an individual.
number of individuals.
number of markers.
a vector with the segregation type of each marker, as
strings.
a vector with the segregation type of each
marker, represented in a simplified manner as integers, i.e. 1
corresponds to markers of type "A"; 2 corresponds to markers
of type "B1.5"; 3 corresponds to markers of type "B2.6";
4 corresponds to markers of type "B3.7"; 5 corresponds to
markers of type "C.8"; 6 corresponds to markers of type
"D1" and 7 corresponds to markers of type "D2"
the name of the input file.
The file format is quite similar to that used by
MAPMAKER/EXP (Lincoln et al., 1993). The first line
contains two integers: the number of individuals and the number of
markers.
Next comes the genotype data for all markers. Each new marker is
initiated with a “*” (without the quotes) followed by the
marker name, without any space between them. Each marker name is
followed by the corresponding segregation type, which may be:
"A.1", "A.2", "A.3", "A.4", "B1.5",
"B2.6", "B3.7", "C.8", "D1.9",
"D1.10", "D1.11", "D1.12", "D1.13",
"D2.14", "D2.15", "D2.16", "D2.17" or
"D2.18" (without quotes) [see marker.type and
Wu et al. (2002) for details].
Finally, after the segregation type comes the genotype data for the
corresponding marker. Depending on the segregation type, genotypes may
be denoted by ac, ad, bc, bd, a,
ba, b, bc, ab and o, in several
possible combinations. To make things easier, we have followed exactly
the notation used by Wu et al. (2002). Genotypes must be
separated by commas. Missing values are denoted by "-"
The example directory in the package distribution contains
an example data file to be read with this function. Further
instructions can be found at the tutorial distributed along with this
package.
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.
Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.
example directory in the package source.
# NOT RUN {
# }
# NOT RUN {
outcr_data <-
read.outcross(dir="work_directory",file="data_file.txt")
# }
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