highScores:
Generate a vector of the highest scoring genes
Description
This function can be used to extract a subset of the highest scoring genes for
other downstream analysis.
Usage
highScores(pvalue_annotation, alpha = 0.05)
Arguments
pvalue_annotation
An S4 object of class PvalueAnnotation for which scoring has already been
performed
alpha
A numeric specifying a threshold at signficant genes can be determined. DEFAULT
is alpha=0.05.
Value
A named vector of scores.
Details
This function randomly samples the scores with replacement 100 times and for
within each random sample for each score it determines the proportion of scores
at or greater than the score. The average of these proportions over the 100
samples will be the new p-value/scores. All scores falling below the threshold
will be returned.
data(test_annotation_score_data)
## Note: commented out for example. See vignette for better example ###out <- highScores(pvalue_annotation=test_annotation, alpha=0.01)