miRNApath (version 1.32.0)

filtermirnapath: Filter miRNApath data

Description

This method filters the miRNApath data to denote hits versus non-hits, the required distinction for running the enrichment algorithm. Data is expected to have been loaded by the loadmirnapath method.

Usage

filtermirnapath(mirnaobj, pvalue=NA, expression=NA, foldchange=NA)

Arguments

mirnaobj

An object of type mirnapath containing data resulting from the loadmirnapath method.

pvalue

If a p-value column has been defined in the mirnapath object, this value is used to define a subset of entries within the dataset which will be denoted as hits.

expression

If an expression column has been defined in the mirnapath object, this value will be used to define entries with expression above this expression level as hits.

foldchange

If a fold change column has been defined in the mirnapath object, this value is used to require hits to have a fold change greater than or equal to this value. The fold change is evaluated in both the positive and the negative, such that a foldchange=2 will allow foldchange=2 and foldchange=-2.

Value

Object of type mirnapath. The state of the object will reflect that the data has been filtered.

Details

This method takes a mirnapath object and assigns a flag for hits and non-hits, depending upon what filter criteria was provided. If multiple criteria are provided, they will all be collectively applied such that all criteria must be fulfilled. To that end, multiple calls to this function on the same mirnapath object should successively shrink the list of hits dependent upon the given criteria.

References

John Cogswell (2008) Identification of miRNA changes in Alzheimer's disease brain and CSF yields putative biomarkers and insights into disease pathways, Journal of Alzheimer's Disease 14, 27-41.

See Also

loadmirnapath, filtermirnapath, loadmirnatogene, loadmirnapathways

Examples

## Load miRNA expression data from AD miRNA paper
## This data contains miRNA expression data, 
data(mirnaobj);

## Display the state, which should generally be "unfiltered"
## at this point
mirnaobj@state;

## Display summary information about the object
mirnaobj;

## Annotate hits by filtering by P-value 0.05
mirnaobj <- filtermirnapath( mirnaobj, pvalue = 0.05,
    expression = NA, foldchange = NA );

## Display summary, noting the state is "filtered"
mirnaobj;