qtl2_to_cape: Convert qtl2 object to cape format

Description Usage Arguments Value References Examples

View source: R/qtl2_to_cape.R

Description

This function converts a data object constructed by qtl2 using the read_cross() function to cape format. It returns a list in which the first element is the cape data object, and the second element is the cape genotype object.

Usage

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qtl2_to_cape(cross, genoprobs = NULL, map = NULL, covar = NULL, verbose = TRUE)

Arguments

cross

a cross object created by the R/qtl2 function read_cross()

genoprobs

an optional argument for providing previously calculated genoprobs. if this parameter is missing, genoprobs are calculated by qtl_to_cape.

map

The qtl2 map. This can be omitted if the map is included in the cross object as either pmap or gmap. By default the physical map (pmap) is used. If it is missing, the genetic map is used. A provided map will be used preferentially over a map included in the cross object.

covar

Optional matrix of any covariates to be included in the analysis.

verbose

A logical value indicating whether to print progress to the screen. Defaults to TRUE.

Value

This function returns a list of two elements. The first element is a cape data object. The second element is a cape genotype object.

References

Carter, G. W., Hays, M., Sherman, A., & Galitski, T. (2012). Use of pleiotropy to model genetic interactions in a population. PLoS genetics, 8(10), e1003010. doi:10.1371/journal.pgen.1003010

Broman, Karl W., Daniel M. Gatti, Petr Simecek, Nicholas A. Furlotte, Pjotr Prins, Ĺšaunak Sen, Brian S. Yandell, and Gary A. Churchill. "R/qtl2: software for mapping quantitative trait loci with high-dimensional data and multiparent populations." Genetics 211, no. 2 (2019): 495-502.

Examples

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## Not run: 
data_obj <- qtl2_to_cape(cross_obj, genoprobs, map, covar, verbose = TRUE)

## End(Not run)

cape documentation built on Feb. 10, 2021, 5:06 p.m.