annotateExpression: Adding expression data to a PvalueAnnotation

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

Description

This function is used to create and load an ExpressionSet into a PvalueAnnotation. Using specified effect and p-value column or named columns that the function will use to determine the effect and p-value columns, it loads the data it into the PvalueAnnotation.

Usage

annotateExpression(pvalue_annotation, expr_data, effect_col = NULL, pval_col = NULL)

Arguments

pvalue_annotation	An S4 object of class PvalueAnnotation
expr_data	An object of class data.frame or matrix with row names corresponding to genes and atleast two columns with an effect and p-value for expression.
effect_col	A numeric specifying the column with an effect direction. If not specified the function will grep for a single named column from: "effect", "odds", "coeff" or "B"
pval_col	A numeric specifying the column with p-values. If not specified the function will grep for a single named column from: "pval","p.val","p_val" or "sig"

Details

The function will load the entire given expression dataset as an ExpressionSet in the expression slot,while the effect and p-value data will also be stored as an "AnnotatedDataFrame" in the phenoData slot of the ExpressionSet.

Value

A PvalueAnnotation, an S4 object with the slot "expression" filled in.

Author(s)

N. Ari Wijetunga

See Also

annotateModification makePvalueAnnotation createPvalueObject

Examples

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

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

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

SMITE documentation built on Nov. 8, 2020, 5:14 p.m.