extractExpression: View the expression data stored in a PvalueAnnotation

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

Description

This function allows the user to see the effect and p-value data that was loaded into a PvalueAnnotation before performing downstream analysis.

Usage

extractExpression(pvalue_annotation)

Arguments

pvalue_annotation

An S4 object of class PvalueAnnotation for which expression data has already been loaded via annotateExpression

Value

A data.frame pulled from the phenoData of the expression slot within a load PvalueAnnotation. The phenoData specifically hold the effect and p-value information.

Author(s)

N. Ari Wijetunga

See Also

annotateExpression

Examples

data(test_annotation_score_data)
data(curated_expressiondata)
## Load Expression data into PvalueAnnotation ##
test_annotation<-annotateExpression(test_annotation, expression_curated)

## Extract entire ExpressionSet with expression data ##
#slot(test_annotation,"expression")

## Extract expression data summary ##
head(extractExpression(pvalue_annotation=test_annotation))

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