compareAgainstReference {cTRAP} | R Documentation |
Compare multiple methods and rank reference accordingly
compareAgainstReference(diffExprGenes, reference, method = c("spearman", "pearson", "gsea"), geneSize = 150, cellLines = NULL, cellLineMean = "auto", rankByAscending = TRUE, rankPerCellLine = FALSE)
diffExprGenes |
Numeric: named vector of differentially expressed genes whose names are gene identifiers and respective values are a statistic that represents significance and magnitude of differentially expressed genes (e.g. t-statistics) |
reference |
Data matrix or |
method |
Character: comparison methods to run ( |
geneSize |
Number: top and bottom number of differentially expressed
genes for gene set enrichment (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 (TRUE) or descending (FALSE) order? |
rankPerCellLine |
Boolean: when ranking results, also rank them based on
individual cell lines instead of only focusing on the mean score across
cell lines; if |
List of data frame containing the results per methods of comparison