read.outcross2: 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

This version implements the read.outcross function in a faster way. Everything else is essentially the same.

Usage

read.outcross2(infile)

Arguments

infile

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"
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.outcross2("data_file.txt")
  
## End(Not run)

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