Differential expression analysis with DESeq2

Description

This function does differential expression analysis with DESeq2-package using the specific formula. It will return a DESeqDataSet object.

Usage

isoDE(ids, formula, ...)

Arguments

Details

First, this function collapses all isomiRs in different types. Read more at isoCounts to know the different options available to collapse isomiRs.

After that, DESeq2-package is used to do differential expression analysis. It uses the count matrix and design experiment stored at (counts(ids) and colData(ids)) IsomirDataSeq object to construct a DESeqDataSet object.

Value

DESeqDataSet object. To get the differential expression isomiRs, use results from DESeq2 package. This allows to ask for different contrast without calling again isoDE. Read results manual to know how to access all the information.

Examples

data(mirData)
ids <- isoCounts(mirData, minc=10, mins=6)
dds <- isoDE(mirData, formula=~condition)

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(isomiRs)
Loading required package: DiscriMiner
Loading required package: IRanges
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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/isomiRs/isoDE.Rd_%03d_medium.png", width=480, height=480)
> ### Name: isoDE
> ### Title: Differential expression analysis with DESeq2
> ### Aliases: isoDE
> 
> ### ** Examples
> 
> data(mirData)
> ids <- isoCounts(mirData, minc=10, mins=6)
> dds <- isoDE(mirData, formula=~condition)
converting counts to integer mode
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>