rankAgainstReference {cTRAP} | R Documentation |
Compare multiple methods and rank against reference accordingly
rankAgainstReference( input, reference, method = c("spearman", "pearson", "gsea"), geneSize = 150, cellLines = NULL, cellLineMean = "auto", rankByAscending = TRUE, rankPerCellLine = FALSE, threads = 1, chunkGiB = 1, verbose = FALSE )
input |
|
reference |
Data matrix or |
method |
Character: comparison method ( |
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 rows with the mean of |
rankByAscending |
Boolean: rank values based on their ascending
( |
rankPerCellLine |
Boolean: rank results based on both individual cell
lines and mean scores across cell lines ( |
threads |
Integer: number of parallel threads |
chunkGiB |
Numeric: if second argument is a path to an HDF5 file
( |
verbose |
Boolean: print additional details? |
Data table with correlation and/or GSEA score results
If a file path to a valid HDF5 (.h5
) file is provided instead of a
data matrix, that file can be loaded and processed in chunks of size
chunkGiB
, resulting in decreased peak memory usage.
The default value of 1 GiB (1 GiB = 1024^3 bytes) allows loading chunks of ~10000 columns and
14000 rows (10000 * 14000 * 8 bytes / 1024^3 = 1.04 GiB
).
When method = "gsea"
, weighted connectivity scores (WTCS) are
calculated (https://clue.io/connectopedia/cmap_algorithms).