Nothing
run_Cuffdiff <- function(counts, conds, cutoff, n, runID) {
res <- Cuffdiff(counts, length(conds[conds == "N"]),
length(conds[conds == "T"]))
resSig <- res[res$pValue < cutoff, ]
# Preparing results to return
result <- new("Result")
result@data <- res[order(as.numeric(res$pValue)), ]
result@id <- result@data$id
result@pval <- as.numeric(result@data$pValue)
return(result)
}
run_Cuffdiff_uqn <- function(counts, conds, cutoff, n, runID) {
res <- Cuffdiff_uqn(counts, length(conds[conds == "N"]),
length(conds[conds == "T"]))
resSig <- res[res$pValue < cutoff, ]
# Preparing results to return
result <- new("Result")
result@data <- res[order(as.numeric(res$pValue)), ]
result@id <- result@data$id
result@pval <- as.numeric(result@data$pValue)
return(result)
}
run_Cuffdiff_Mode <- function(counts, conds, cutoff, n, runID,
winSize) {
res <- Cuffdiff_Mode(counts, conds, length(conds[conds ==
"N"]), length(conds[conds == "T"]), runID, winSize)
resSig <- res[res$pValue < cutoff, ]
# Preparing results to return
result <- new("Result")
result@data <- res[order(as.numeric(res$pValue)), ]
result@id <- result@data$id
result@pval <- as.numeric(result@data$pValue)
return(result)
}
run_Cuffdiff_nde <- function(counts, DElist, conds, cutoff, n,
runID) {
res <- Cuffdiff_nde(counts, DElist, length(conds[conds ==
"N"]), length(conds[conds == "T"]), runID)
resSig <- res[res$pValue < cutoff, ]
# Preparing results to return
result <- new("Result")
result@data <- res[order(as.numeric(res$pValue)), ]
result@id <- result@data$id
result@pval <- as.numeric(result@data$pValue)
return(result)
}
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