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Last data update: 2014.03.03

R: Filter miRNApath data

filtermirnapath

R Documentation

Filter miRNApath data

Description

This method filters the miRNApath data to denote hits versus non-hits, the required distinction for running the enrichment algorithm. Data is expected to have been loaded by the loadmirnapath method.

Usage

filtermirnapath(mirnaobj, pvalue=NA, expression=NA, foldchange=NA)

Arguments

`mirnaobj`	An object of type mirnapath containing data resulting from the `loadmirnapath` method.
`pvalue`	If a p-value column has been defined in the mirnapath object, this value is used to define a subset of entries within the dataset which will be denoted as hits.
`expression`	If an expression column has been defined in the mirnapath object, this value will be used to define entries with expression above this expression level as hits.
`foldchange`	If a fold change column has been defined in the mirnapath object, this value is used to require hits to have a fold change greater than or equal to this value. The fold change is evaluated in both the positive and the negative, such that a foldchange=2 will allow foldchange=2 and foldchange=-2.

Details

This method takes a mirnapath object and assigns a flag for hits and non-hits, depending upon what filter criteria was provided. If multiple criteria are provided, they will all be collectively applied such that all criteria must be fulfilled. To that end, multiple calls to this function on the same mirnapath object should successively shrink the list of hits dependent upon the given criteria.

Value

Object of type mirnapath. The state of the object will reflect that the data has been filtered.

Note

The method attempts to convert fold change columns appropriately so that filtering by 2 will properly mark entries greater than 2, less than -2, or less than 0.5, as the case may be.

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);

## 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 );

## Display summary, noting the state is "filtered"
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.
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Type 'license()' or 'licence()' for distribution details.

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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
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Type 'q()' to quit R.

> library(miRNApath)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/miRNApath/filtermirnapath.Rd_%03d_medium.png", width=480, height=480)
> ### Name: filtermirnapath
> ### Title: Filter miRNApath data
> ### Aliases: filtermirnapath
> ### Keywords: manip
> 
> ### ** 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 );
> 
> ## Display summary, noting the state is "filtered"
> 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 
>