qtl (version 1.66)

addloctocross: Add phenotype location into a cross object

Description

Add phenotype location(s) into a cross object (with eQTL/pQTL studies)

Usage

addloctocross(cross, locations=NULL, locfile="locations.txt", verbose=FALSE)

Value

The input cross object, with the locations added as an additional component locations

Arguments

cross

An object of class cross. See read.cross for details.

locations

R variable holding location information

locfile

load from a file, see the details section for the layout of the file.

verbose

If TRUE, give verbose output

Author

Ritsert C Jansen; Danny Arends; Pjotr Prins; Karl W Broman

Details

inputfile layout: Num Name Chr cM 1 X3.Hydroxypropyl 4 50.0 Num is the number of the phenotype in the cross object Name is the name of the phenotype (will be checked against the name already in the cross object at position num Chr Chromosome cM position from start of chromosome in cM

See Also

• mqmplot.cistrans - Cis/trans plot

• The MQM tutorial: https://rqtl.org/tutorials/MQM-tour.pdf

• MQM - MQM description and references

• mqmscan - Main MQM single trait analysis

• mqmscanall - Parallellized traits analysis

• mqmaugment - Augmentation routine for estimating missing data

• mqmautocofactors - Set cofactors using marker density

• mqmsetcofactors - Set cofactors at fixed locations

• mqmpermutation - Estimate significance levels

• scanone - Single QTL scanning

Examples

if (FALSE) {
    data(multitrait)
    data(locations)
    multiloc <- addloctocross(multitrait,locations)
    results <- scanall(multiloc)
    mqmplot.cistrans(results, multiloc, 5, FALSE, TRUE)
  }