onemap (version 2.0-1)

read.outcross: Read data from a segregating full-sib population

Description

Imports data from a full-sib family derived from the cross of two outbred parents and creates an object of class outcross.

Usage

read.outcross(dir, file)

Arguments

dir

directory where the input file is located.

file

the name of the input file which contains the data to be read.

Value

• An object of class outcross, i.e., a list with the following components:
• geno
  a matrix with integers indicating the genotypes read for each marker. 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.
• segr.type.num
  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"
• input
  the name of the input file.

Details

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.

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.

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.

See Also

example directory in the package source.

Examples

outcr_data <-
read.outcross(dir="work_directory",file="data_file.txt")