compEpiTools (version 1.6.3)

makeGtfFromDb-methods: Utilities to transform a TxDb into a GTF file

Description

Given a TxDB, the method 'makeGtfFromDb' creates and writes to file a GTF file of exons either at the gene level or at the transcript level. This methods can be used to generate a GTF file that is compliant with Bioconductor TxDB libraries, to be used for example with external tools for counting NGS reads over genes or transcripts. The method 'featuresLength' determines the length of all the features associated to every gene or transctipt and returns the sum. All the exons associated to either a gene or a transcript are non-overlapping. This can be useful to determine read counts into summaries such as expression RPKMs.

Methods

The 'makeGtfFromDb' has to be used in this form: makeGtfFromDb(object, type, filename) where:

• object: TxDb
• type: character, either 'gene' or 'tx'
• filename: either NULL (a data.frame is returned) or a character containing the path to the file that has to be written

The 'featuresLength' has to be used in this form: featuresLength(object, type) where:

• object: TxDb
• type: character, either 'gene' or 'tx'

It returns a vector of integers with number of items equal to the number genes or transcripts annotated in the TxDb given containing the widths of the features.

Examples

require(TxDb.Mmusculus.UCSC.mm9.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
isActiveSeq(txdb) <- c(TRUE, rep(FALSE, length(isActiveSeq(txdb)) - 1))
chr1geneLengths <- featuresLength(txdb, 'gene')
res <- makeGtfFromDb(txdb, 'gene')
isActiveSeq(txdb) <- rep(TRUE, length(isActiveSeq(txdb)))