read.outcross: Read data from a full-sib progeny (outcrossing populations)

In bschiffthaler/BatchMap: Software for the Creation of High Density Linkage Maps in Outcrossing Species

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.

Details

The file format is quite similar to that used by MAPMAKER/EXP (Lincoln et al., 1993). The first line contains three integers: the number of individuals, the number of markers and the number of traits.

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].

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 "-"

Finally, if there is phenotypic data, it will be added just after the marker data. They need to be separated by commas as well, using the same symbol for missing information.

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 the package.

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"
n.phe	the number of traits included in the file
pheno	the name of the phenoytpes
input	the name of the input file.

Author(s)

Adapted from Karl Broman (package qtl) by Gabriel R A Margarido, [e-mail], later with additions from Luciano C Silva

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

  ## Not run: 
    outcr_data <-
read.outcross(dir="work_directory",file="data_file.txt")
  
## End(Not run)

bschiffthaler/BatchMap documentation built on Dec. 16, 2019, 2:22 a.m.