compareWithAllMethods {cTRAP} | R Documentation |
Compare reference using all methods
compareWithAllMethods( method, input, reference, geneSize = 150, cellLines = NULL, cellLineMean = "auto", rankPerCellLine = FALSE, threads = 1, chunkGiB = 1, verbose = FALSE )
method |
Character: comparison method ( |
input |
|
reference |
Data matrix or |
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 |
rankPerCellLine |
Boolean: rank results based on both individual cell
lines and mean scores across cell lines ( |
threads |
Integer: number of parallel threads |
chunkGiB |
Numeric: size (in gibibytes) of chunks to load
|
verbose |
Boolean: print additional details? |
rankByAscending |
Boolean: rank values based on their ascending
( |
List of data tables with correlation and/or GSEA score results
When method = "gsea"
, weighted connectivity scores (WTCS) are
calculated (https://clue.io/connectopedia/cmap_algorithms).