annotatePC {GenomicSuperSignature} | R Documentation |
This function finds the RAV scored highest with the top PCs of the dataset, including RAVs with the negative average silhouette.
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)