I/NI filtering of a DEXUS result.

Description

This function filters the result object for informative transcripts. Transcripts with an I/NI value below the given threshold are filtered out.

Arguments

Value

An instance of "DEXUSResult".

Author(s)

Guenter Klambauer klambauer@bioinf.jku.at and Thomas Unterthiner unterthiner@bioinf.jku.at

Examples

data(dexus)
res <- dexus(countsBottomly[1:100, ])
INI(res)

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)

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> library(dexus)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'dexus'

The following object is masked from 'package:BiocGenerics':

    sizeFactors

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/dexus/INI.Rd_%03d_medium.png", width=480, height=480)
> ### Name: INI
> ### Title: I/NI filtering of a DEXUS result.
> ### Aliases: INI
> 
> ### ** Examples
> 
> data(dexus)
> res <- dexus(countsBottomly[1:100, ])
Filtered out 5 % of the genes due to low counts
Unsupervised mode.
> INI(res)
Total number of transcripts:  100 
Number of differentially expressed transcripts:  5 
Percentage of differentially expressed transcripts:  5 % 

Displaying the 10 top ranked genes of the analyis: 
  Index         Transcript INIcall   INI Mean.Condition_1 Mean.Condition_2
1     1 ENSMUSG00000000544    TRUE 1.899             34.1              0.6
2     2 ENSMUSG00000000486    TRUE 0.351              9.7              2.1
3     3 ENSMUSG00000000355    TRUE 0.215            271.5            128.1
4     4 ENSMUSG00000000552    TRUE 0.144            749.5           1094.5
5     5 ENSMUSG00000000392    TRUE 0.122             24.5              1.8

Total number of transcripts:  5 
Number of differentially expressed transcripts:  5 
Percentage of differentially expressed transcripts:  100 % 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>