highScores: Generate a vector of the highest scoring genes

In GreallyLab/SMITE: Significance-based Modules Integrating the Transcriptome and Epigenome

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.

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.

Value

A named vector of scores.

Author(s)

N. Ari Wijetunga

See Also

scorePval plotCompareScores runSpinglass runBioNet

Examples

data(test_annotation_score_data)


## Note: commented out for example.  See vignette for better example ##

#out <- highScores(pvalue_annotation=test_annotation, alpha=0.01)

GreallyLab/SMITE documentation built on May 6, 2019, 6:30 p.m.