runLOLA results table for PEP databases

[joseverdezoto]

As of now, the runLOLA() results table displays columns defined in the index.txt file (e.g tissue, antibody). If the PEP sample annotation sheet doesn't contain those fields, the overlaps and fisher scores can be calculated but the function will crash when writing the results table.

Perhaps we could make this aspect of runLOLA() more flexible so that it accepts any fields the user provides in the PEP sample_annotation.csv file.

LOLA/R/calcLocEnrichment.R

Lines 180 to 185 in 6d5111a

	orderedCols = c("userSet", "dbSet", "collection", "pValueLog", "oddsRatio",
	"support", "rnkPV", "rnkOR", "rnkSup", "maxRnk", "meanRnk", "b", "c", "d",
	"description", "cellType", "tissue", "antibody", "treatment", "dataSource", "filename")
	unorderedCols = setdiff(colnames(scoreTable), orderedCols)
	setcolorder(scoreTable, c(orderedCols, unorderedCols))