Set the I/NI threshold.

Description

This generic function sets the threshold of the I/NI value. Transcripts with I/NI values above the I/NI threshold are considered as differentially expressed. The results of DEXUS are stored as an instance of DEXUSResult-class.

Arguments

Value

INIThreshold<- returns an instance of "DEXUSResult".

Author(s)

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

Examples

data(dexus)
result <- dexus(countsBottomly[1:20,1:10])
INIThreshold(result) <- 0.1

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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Type 'demo()' for some demos, 'help()' for on-line help, or
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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/INIThreshold-set.Rd_%03d_medium.png", width=480, height=480)
> ### Name: INIThreshold<-
> ### Title: Set the I/NI threshold.
> ### Aliases: INIThreshold<- INIThreshold-set
> 
> ### ** Examples
> 
> data(dexus)
> result <- dexus(countsBottomly[1:20,1:10])
Filtered out 10 % of the genes due to low counts
Unsupervised mode.
> INIThreshold(result) <- 0.1
Total number of transcripts:  20 
Number of differentially expressed transcripts:  1 
Percentage of differentially expressed transcripts:  5 % 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>