filtermirnapath: Filter miRNApath data
In miRNApath: miRNApath: Pathway Enrichment for miRNA Expression Data

Description Usage Arguments Details Value Note Author(s) References See Also Examples

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.

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

`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.

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.

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

The method attempts to convert fold change columns appropriately so that filtering by 2 will properly mark entries greater than 2, less than -2, or less than 0.5, as the case may be.

James M. Ward jmw86069@gmail.com

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.

loadmirnapath, filtermirnapath, loadmirnatogene, loadmirnapathways

## 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;