scan_qtl2_to_qtl {qtl2convert} | R Documentation |
Convert scan1 results to the scanone format
Description
Convert the results of qtl2::scan1()
to the form used by the R/qtl function
qtl::scanone()
.
Usage
scan_qtl2_to_qtl(scan1_output, map)
Arguments
scan1_output |
Matrix of LOD scores, as calculated by
|
map |
Map of markers/pseudomarkers (as a list of vectors). |
Value
A data frame with class "scanone"
, containing
chromosome and position columns followed by the LOD scores in
scan1_output
.
See Also
Examples
library(qtl2)
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
map <- insert_pseudomarkers(iron$gmap, step=1)
probs <- calc_genoprob(iron, map, error_prob=0.002)
pheno <- iron$pheno
covar <- match(iron$covar$sex, c("f", "m")) # make numeric
names(covar) <- rownames(iron$covar)
Xcovar <- get_x_covar(iron)
out <- scan1(probs, pheno, addcovar=covar, Xcovar=Xcovar)
out_rev <- scan_qtl2_to_qtl(out, map)
[Package qtl2convert version 0.30 Index]