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

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.

Value

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

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.

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;

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/loadmirnatogene.Rd_%03d_medium.png", width=480, height=480)
> ### Name: loadmirnatogene
> ### Title: Load miRNA to gene associations for miRNApath
> ### Aliases: loadmirnatogene
> ### Keywords: IO manip attribute
> 
> ### ** 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;
[1] "filtered"
> 
> ## Display summary information about the object
> 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 
> 
> ## 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;
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 
>