readCuffGeneFpkm: Reads FPKM values into ExpressionSet.

In spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

Description

Opens fpkm_tracking files and collects FPKM values into ExpressionSet. The function is intended to work whith genes.fpkm_tracking files. In order to get unique gene identifier, the contained values are grouped and for each gene the maximum FPKM values is selected. There should only be a few hundred multiple occurring genes and the maximum value should give a (slight) underestimation of the real value.

Usage

readCuffGeneFpkm(cuff, phenoData, summ="max")

Arguments

cuff	character: Vector of cufflinks files

phenoData

AnnotatedDataFrame: Requirement for construction of an ExpressionSet

summ	character: Must be either 'max' or 'sum'. A handful of tracking id's occur multiple times due to multiple transcripts which partially are non-overlapping. The summ (summarize) Argument determines the way the multiplets are handled.

Value

ExpressionSet

Author(s)

Wolfgang Kaisers

Examples

n<-10
cuff <- system.file("extdata", "cuff_files",
    paste(1:n, "genes", "fpkm_tracking", sep="."), package="spliceSites")

## Create Pheno - data
gr <- system.file("extdata", "cuff_files", "groups.csv", package="spliceSites")
groups <- read.table(gr, sep="\t", header=TRUE)
meta <- data.frame(labelDescription=c("gender", "age-group", "location"),
            row.names=c("gen", "agg", "loc"))
phenoData <- new("AnnotatedDataFrame", data=groups, varMetadata=meta)

## Read ExpressionSet
exset <- readCuffGeneFpkm(cuff, phenoData)

Example output

Loading required package: rbamtools
Loading required package: refGenome
Loading required package: doBy
Loading required package: RSQLite
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, cbind, colMeans, colSums, 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, 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: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

[ 1/10]	probe: exp_1
[ 2/10]	probe: exp_2
[ 3/10]	probe: exp_3
[ 4/10]	probe: exp_4
[ 5/10]	probe: exp_5
[ 6/10]	probe: exp_6
[ 7/10]	probe: exp_7
[ 8/10]	probe: exp_8
[ 9/10]	probe: exp_9
[10/10]	probe: exp_10

spliceSites documentation built on May 6, 2019, 3:05 a.m.