read.mpcross: Construct mpcross objects from datafiles

Description Usage Arguments See Also

View source: R/read.mpcross.R

Description

Generate an mpcross object by reading in components from files - requires founders marker data, finals marker data, pedigree, and IDs for all lines. Marker map and phenotypic data are optional.

Usage

1
2
  read.mpcross(founderfile, finalfile, pedfile, mapfile,
    phenofile)

Arguments

founderfile

File containing founder genotypes - should have 1+(number of founders) columns. The first column contains the marker names - first space left blank. The first row for the other columns contains the founder name. Additional rows contain observed marker data for all founders.

finalfile

File containing final genotypes - should have 1+(number of lines) columns. The first column contains the marker names - first space left blank. The first row for the other columns contains line names. Additional rows contain observed marker data for all lines.

pedfile

File containing pedigree data - should have three or four columns - first three columns indicate id, mother and father; fourth column is a flag for whether the lines was observed.

mapfile

File containing linkage map - should contain three columns - one for marker names, one for chromosome assignment and one for map position in cM

phenofile

File containing phenotypic data - should contain one column for each phenotype, with rows indexing lines.

See Also

sim.mpcross, mpcross


mpMap documentation built on May 29, 2017, 2:50 p.m.