Analyze biological interpretations of metagene
Identify the biological pathways (gene sets from Reactome) that each metagene (factor) might belongs to.
runGSEA( object, gene_sets = c(), mat_w = TRUE, mat_v = 0, custom_gene_sets = c() )
object |
|
gene_sets |
A list of the Reactome gene sets names to be tested. If not specified, this function will use all the gene sets from the Reactome by default |
mat_w |
This indicates whether to use the shared factor loadings 'W' (default TRUE) |
mat_v |
This indicates which V matrix to be added to the analysis. It can be a numeric number or a list of the numerics. |
custom_gene_sets |
A named list of character vectors of entrez gene ids. If not specified, this function will use all the gene symbols from the input matrix by default |
A list of matrices with GSEA analysis for each factor
## Not run: # ligerex (liger object), factorization complete wilcox.results <- runGSEA(ligerex) wilcox.results <- runGSEA(ligerex, mat_v = c(1, 2)) ## End(Not run)
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