diff --git a/R/readErmineJOutput.R b/R/readErmineJOutput.R index c39f380..c4556fd 100644 --- a/R/readErmineJOutput.R +++ b/R/readErmineJOutput.R @@ -8,16 +8,19 @@ readErmineJOutput = function(output){ fileHead = readLines(output,100,warn = FALSE) dataStart = fileHead %>% grep(x = .,pattern = '#!') %>% max + cn = c("#!", "Name", "ID", "NumProbes", "NumGenes", "RawScore", "Pval", + "CorrectedPvalue", "MFPvalue", "CorrectedMFPvalue", "Multifunctionality", + "Same as", "GeneMembers","") frame = suppressMessages(suppressWarnings( - readr::read_tsv(output,skip = dataStart-1,col_names=TRUE) + readr::read_tsv(output,skip = dataStart,col_names=cn) )) if(!is.numeric(frame$Pval)){ frame = suppressMessages(suppressWarnings( - readr::read_tsv(output,skip = dataStart-1,col_names=TRUE, locale = readr::locale(decimal_mark = ',')) + readr::read_tsv(output,skip = dataStart,col_names=cn, locale = readr::locale(decimal_mark = ',')) )) } - frame = frame[1:(nrow(frame)-1),2:ncol(frame)] + frame = frame[,2:(ncol(frame)-1)] settingsStart = fileHead %>% grep(x = .,pattern = 'Settings') settingsEnd = fileHead %>% grep(x = .,pattern = '#!----')