qtl2_to_cape: Convert qtl2 object to cape format
In cape: Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice
qtl2_to_cape R Documentation
Convert qtl2 object to cape format
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
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, Śaunak 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.
cape documentation built on May 29, 2024, 5:11 a.m.
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| qtl2_to_cape | R Documentation |
Convert qtl2 object to cape format
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
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, Śaunak 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.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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