loadmirnatogene: Load miRNA to gene associations for miRNApath
In miRNApath: miRNApath: Pathway Enrichment for miRNA Expression Data

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

This method loads associations between miRNAs to the genes they affect.

1 2	loadmirnatogene(mirnafile, mirnaobj, mirnacol="miRNA Name", genecol="Entrez Gene ID", columns=NA)

`mirnafile`	The tab-delimited miRNA results file to be loaded. The file is expected to be in tall-skinny format.
`mirnaobj`	An object of type mirnapath containing data resulting from the `loadmirnapath` method.
`mirnacol`	The name of the column header which contains the miRNA names being assayed. That is, the name of the column header in the file being read.
`genecol`	The name of the column header which contains the gene names being assayed.
`columns`	The names of any additional columns in the file being read which should equate with the mirnapath object.

The data is expected to have miRNA names which exactly match those in the mirnaTable item of the mirnapath object. Also, the gene names are expected to match exactly with those gene names loaded by loadmirnapathways.

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.

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 );

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

## Load the miRNA to gene associations
mirnaobj <- loadmirnatogene( mirnafile = "mirnaGene.txt",
    mirnaobj = mirnaobj, mirnacol = "miRNA Name",
    genecol = "Entrez Gene ID", 
    columns = c(assayidcol = "ASSAYID") );

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