readCuffGeneFpkm: Reads FPKM values into ExpressionSet.

In wokai/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)

wokai/spliceSites documentation built on May 4, 2019, 9:46 a.m.