readCuffGeneFpkm {spliceSites} | R Documentation

## Reads FPKM values into ExpressionSet.

### 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)

[Package spliceSites version 1.28.0 Index]