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## convert_scanone
## Karl W Broman
# Convert scanone output to a list format for interactive visualization
#
# Convert the results of a single-QTL genome scan, as output by
# \code{\link[qtl]{scanone}}, to a list format, for use with
# interactive graphics, such as \code{\link{iplotScanone}}.
# (Largely for internal use.)
#
# @param output An object of class \code{"scanone"}, as output by
# \code{\link[qtl]{scanone}}.
# @param lod_as_matrix If TRUE, keep lod scores as a matrix; if FALSE, make a vector
#
# @return A list with the data reformatted
#
# @keywords interface
#
# @examples
# library(qtl)
# data(hyper)
# hyper <- calc.genoprob(hyper, step=1)
# out <- scanone(hyper)
# out_as_list <- convert_scanone(out)
convert_scanone <-
function(output, lod_as_matrix=TRUE)
{
# marker names: replace pseudomarkers with blanks
mnames <- rownames(output)
pmarkers <- grep("^c.+\\.loc-*[0-9]+", mnames)
mnames[pmarkers] <- ""
# chromosome IDs factor -> character
output[,1] <- as.character(output[,1])
# chromosome names
chrnames <- unique(output[,1])
# lod scores
if(lod_as_matrix) {
lod <- as.matrix(output[,-(1:2)])
dimnames(lod) <- NULL
}
else {
lod <- output[,3]
names(lod) <- NULL
}
# lod column names
lodnames <- names(output)[-(1:2)]
if(length(lodnames) != length(unique(lodnames)))
warning("lod column names are not unique")
list(chr=as.character(output[,1]),
pos=output[,2],
lod=lod,
marker=mnames,
chrname=chrnames,
lodname=lodnames)
}
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