compareAgainstReference {cTRAP} | R Documentation |
Compare multiple methods and rank reference accordingly
compareAgainstReference( input, reference, method = c("spearman", "pearson", "gsea"), geneSize = 150, cellLines = NULL, cellLineMean = "auto", rankByAscending = TRUE, rankPerCellLine = FALSE )
input |
|
reference |
Data matrix or |
method |
Character: one or more methods to compare data
( |
geneSize |
Numeric: number of top up-/down-regulated genes to use as
gene sets to test for enrichment in reference data; if a 2-length numeric
vector, the first index is the number of top up-regulated genes and the
second index is the number of down-regulated genes used to create gene
sets; only used if |
cellLines |
Integer: number of unique cell lines |
cellLineMean |
Boolean: add a column with the mean score across cell
lines? If |
rankByAscending |
Boolean: rank values based on their ascending
( |
rankPerCellLine |
Boolean: rank results based on both individual cell
lines and mean scores across cell lines ( |
List of data frame containing the results per methods of comparison