annotatePC {GenomicSuperSignature} | R Documentation |
This function finds the RAV with the highest validation score (including RAVs with negative silhouette width) for specified PC of the dataset and returns the top enriched pathways.
annotatePC( PCnum, val_all, RAVmodel, n = 5, scoreCutoff = 0.5, nesCutoff = NULL, simplify = TRUE, abs = FALSE, trimed_pathway_len = 45 )
PCnum |
A numeric vector. PC number of your dataset that you want to get
the annotation results. The vector can contain any integer number among
|
val_all |
The output from |
RAVmodel |
The RAVmodel used to generate the input for the argument,
|
n |
An integer. Default is 5. The number of the top enriched pathways
to print out. If there are fewer than n pathways passed the cutoff, it will
print out |
scoreCutoff |
A numeric value for the minimum correlation. Default is 0.5. |
nesCutoff |
A numeric value for the minimum NES. Default is |
simplify |
A logical. Under default ( |
abs |
Default is |
trimed_pathway_len |
Positive inter values, which is the display width of pathway names. Default is 45. |
A data frame of a list based on the simplify
argument. Check
the output detail above.
data(miniRAVmodel) library(bcellViper) data(bcellViper) val_all <- validate(dset, miniRAVmodel) annotatePC(2, val_all, miniRAVmodel)