Nothing
##
## Accessor methods for MeSHHyperParams class
##
## check MeSHHyperParams instance for validity.
## If we can fix it, we do (and issue a warning)
## Return a more valid instance or error
## Based on Category/R/HyperGParams-accessors.R
.makeValidMeSHParams <- function(object) {
##
## Validation of MeSH version
##
if(meshVersion(MeSH.db)[1,2] != meshVersion(eval(parse(text=object@annotation)))[1,2]){
stop("\n#############################################################################\nMeSH-version of MeSH.db and MeSH.XXX.eg.db-type packages must be coincided!\nPlease confirm the version of MeSH by typing\n\n'meshVersion(MeSH.db)'\n\n'meshVersion(MeSH.XXX.eg.db)'\n\nand then install appropriate version of these packages\n#############################################################################")
}
##
##
##
sel <- geneIds(object)
if (is.list(sel)) {
warning("converting geneIds from list to atomic vector via unlist")
sel <- unlist(sel)
}
if (any(duplicated(sel))) {
warning("removing duplicate IDs in geneIds")
sel <- unique(sel)
}
geneIds(object) <- sel
univ <- universeGeneIds(object)
if (length(univ)) {
if (is.list(univ)) {
warning("converting univ from list to atomic vector via unlist")
univ <- unlist(univ)
}
if (typeof(sel) != typeof(univ))
stop(paste("geneIds and universeGeneIds must have the same mode\n",
"geneIds:", typeof(sel), "\n",
"universeGeneIds:", typeof(univ)), .Call=FALSE)
if (any(duplicated(univ))) {
warning("removing duplicate IDs in universeGeneIds")
univ <- unique(univ)
}
universeGeneIds(object) <- univ
if (!all(sel %in% univ)) {
warning("removing geneIds not in universeGeneIds")
sel <- intersect(sel, univ)
if (!length(sel))
stop("no geneIds in universeGeneIds", .Call=FALSE)
geneIds(object) <- sel
}
}
pv <- pvalueCutoff(object)
if (pv > 1 || pv < 0){
stop("invalid pvalueCutoff, must be between 0 and 1", .Call=FALSE)}
return(object)
}
## Based on Category/R/HyperGParams-accessors.R
## Generic is defiend in Category/R/AllGenerics.R
setMethod("makeValidParams", "MeSHHyperGParams", .makeValidMeSHParams)
## Based on Category/R/HyperGParams-accessors.R
## Generic is defined in GSEABase/R/AllGenerics.R
setMethod("geneIds", "MeSHHyperGParams", function(object, ...) object@geneIds)
setReplaceMethod("geneIds", "MeSHHyperGParams", function(object, value) {
object@geneIds <- value
object
})
## Based on Category/R/HyperGParams-accessors.R
## Generic is defiend in Category/R/AllGenerics.R
setMethod("universeGeneIds", "MeSHHyperGParams", function(r) r@universeGeneIds)
setReplaceMethod("universeGeneIds", "MeSHHyperGParams", function(r, value) {
r@universeGeneIds <- value
r
})
## Based on Category/R/HyperGParams-accessors.R
## Generic is defiend in Category/R/AllGenerics.R
setMethod("annotation", "MeSHHyperGParams", function(object) object@annotation)
setReplaceMethod("annotation", c("MeSHHyperGParams", "character"),
function(object, value) {
object@annotation <- value
object
})
## Our original
setMethod("category", "MeSHHyperGParams", function(r) r@category)
setReplaceMethod("category", c("MeSHHyperGParams", "character"),
function(r, value) {
r@category <- value
r
})
## Our original
setMethod("database", "MeSHHyperGParams", function(r) r@database)
setReplaceMethod("database", c("MeSHHyperGParams", "character"),
function(r, value) {
r@database <- value
r
})
setMethod("pAdjust", "MeSHHyperGParams", function(r) r@pAdjust)
setReplaceMethod("pAdjust", c("MeSHHyperGParams", "character"),
function(r, value) {
r@pAdjust <- value
r
})
## Based on Category/R/HyperGParams-accessors.R
## Generic is defined in Category/R/AllGeneric.R
setMethod("pvalueCutoff", "MeSHHyperGParams", function(r) r@pvalueCutoff)
setReplaceMethod("pvalueCutoff", "MeSHHyperGParams", function(r, value) {
r@pvalueCutoff <- value
r
})
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.