miRNApath (version 1.32.0)

loadmirnatogene: Load miRNA to gene associations for miRNApath

Description

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

Usage

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

Arguments

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.

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 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.

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 );

## 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;