newReadCountSet: Generate a new ReadCountSet object

In SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Description

This is a internal function to generate a new ReadCountSet object.

Usage

newReadCountSet(readCounts, exonIDs, geneIDs)

Arguments

readCounts	a data frame, read counts for each exon of each samples. Must have colnames, which indicate the label of samples.
exonIDs	a character vector indicating exon IDs.
geneIDs	a character vector indicating gene IDs.

Value

A object of the ReadCountSet class.

Author(s)

Xi Wang, [e-mail]

See Also

loadExonCountData, ReadCountSet-class

Examples

rcounts <- cbind(t(sapply(1:10, function(x) {rnbinom(5, size=10, prob=runif(1))} ) ) , 
                 t(sapply(1:10, function(x) {rnbinom(5, size=10, prob=runif(1))} ) ) )
colnames(rcounts) <- c(paste("S", 1:5, sep=""), paste("C", 1:5, sep="")) 
geneIDs <- c(rep("G1", 4), rep("G2", 6))
exonIDs <- c(paste("E", 1:4, sep=""), paste("E", 1:6, sep=""))
## 
RCS <- newReadCountSet(rcounts, exonIDs, geneIDs)
RCS 
## End

Example output

Loading required package: Biobase
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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

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

Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: DESeq
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.
ReadCountSet (storageMode: environment)
assayData: 10 features, 10 samples 
  element names: counts 
protocolData: none
phenoData
  sampleNames: S1 S2 ... C5 (10 total)
  varLabels: label
  varMetadata: labelDescription
featureData
  featureNames: 1 2 ... 10 (10 total)
  fvarLabels: exonIDs geneIDs ... padjust (10 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  

SeqGSEA documentation built on Nov. 8, 2020, 5:46 p.m.