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Last data update: 2014.03.03

R: Load gene to pathway associations for miRNApath

loadmirnapathways

R Documentation

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.

Details

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

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.

Author(s)

James M. Ward jmw86069@gmail.com

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.

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;

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(miRNApath)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/miRNApath/loadmirnapathways.Rd_%03d_medium.png", width=480, height=480)
> ### Name: loadmirnapathways
> ### Title: Load gene to pathway associations for miRNApath
> ### Aliases: loadmirnapathways
> ### Keywords: IO manip attribute
> 
> ### ** 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;
mirnapath object:
   Length     Class      Mode 
        1 mirnapath        S4 

Columns specified:
   mirnacol = "miRNA Name"
   assayidcol = "ASSAYID"
   groupcol = "GROUP"
   filterflagcol = "FILTERFLAG"
   mirnagene = "miRNA-Gene"
   genecol = "Entrez Gene ID"
   pathwaycol = "Pathway Name"
   pathwayidcol = "PATHWAY_ID"
   pvaluecol = "P-value"
   
Filters Applied:
   none

Number of miRNAs: 196 
Number of sample groups: 18 
Number of pathways: 771 
State: filtered 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>