miRNApath (version 1.32.0)

loadmirnapathways: Load gene to pathway associations for miRNApath

Description

This method loads associations between genes and the pathways to which they belong.

Usage

loadmirnapathways(mirnaobj, pathwayfile, genecol="Entrez Gene ID",
pathwaycol="PATHWAY", columns=c(), pathwayidcol=NA)

Arguments

mirnaobj

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

pathwayfile

The file containing the gene to pathway associations.

genecol

The name of the column header which contains the gene names associated with pathway data.

pathwaycol

The name of the column header which contains the pathway names.

columns

The names of any additional columns in the file being read which should equate with the mirnapath object.

pathwayidcol

The (optional) column header for IDs associated with the pathway names.

Value

The method returns an object of type mirnapath, a list with components:

mirnaTable

data.frame containing the miRNA results data

columns

list containing the names of required column headers associated to the actual column header supplied in the dataset contained in mirnaTable. Required headers: mirnacol, assayidcol. Optional headers: groupcol, pvaluecol, foldchangecol, expressioncol, filterflagcol

groupcount

the number of groups contained in mirnaTable using the groupcol, if supplied

state

the current state of the object, using the following values in order of progress through the typical workflow: unfiltered, filtered, enriched.

Details

The data loaded is expected to have gene names which exactly match those gene names loaded by loadmirnatogene.

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, runEnrichment

Examples

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

## Write a file as example of required input
write.table(mirnaobj@mirnaPathways, file = "mirnaPathways.txt", 
    quote = FALSE, row.names = FALSE, col.names = TRUE, na = "",
    sep = "\t");

## Load the gene to pathway associations
mirnaobj <- loadmirnapathways( mirnaobj = mirnaobj, 
    pathwayfile = "mirnaPathways.txt", 
    pathwaycol = "Pathway Name", genecol = "Entrez Gene ID");

## Display summary, noting the number of genes reported
mirnaobj;