annotateExpression {SMITE} | R Documentation

## Adding expression data to a PvalueAnnotation

### 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))

[Package SMITE version 1.8.0 Index]