checkIfPoolIncludeSample <-
function(model, sampleVector, poolVector = NULL) {
# Chcking if experiment data all in model data.
if (0 != length(poolVector)) {
if (0 != sum(!(sampleVector %in% poolVector))) {
warning("element_names are outside of pool.",
" ",
paste(setdiff(sampleVector, unique(poolVector)), collapse = ", "))
return(setdiff(sampleVector, setdiff(sampleVector, unique(poolVector))))
}
} else {
if (0 != sum(!(sampleVector %in% unique(unlist(
model$listOfValues
))))) {
warning("element_names are outside of gmt.",
" ",
paste(setdiff(sampleVector, unique(
unlist(model$listOfValues)
)),
collapse = ", "))
return(setdiff(sampleVector, setdiff(sampleVector, unique(
unlist(model$listOfValues)
))))
}
}
return(sampleVector)
}
cutGmtToPool <- function(gmt, pool) {
cutDF <- plyr::ddply(
.data = gmt,
.variables = c("ontologyId"),
.fun = function(dfRow) {
dfRow$listOfValues[[1]] <- intersect(dfRow$listOfValues[[1]], pool)
dfRow
}
)
cutDF
}
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