annotateExpression {SMITE} | R Documentation |
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.
annotateExpression(pvalue_annotation, expr_data, effect_col = NULL, pval_col = NULL)
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" |
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.
A PvalueAnnotation, an S4 object with the slot "expression" filled in.
N. Ari Wijetunga
annotateModification makePvalueAnnotation createPvalueObject
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))