reshapeTxDb: Reshape a TranscriptDb object with additional information

In Senbee/Sequgio: Isoform expression estimation based on RNA-seq data

Description

This function process a TranscriptDb-class object disjoining overlapping genomic regions and adding additional information needed for design matrices building and fitting.

Usage

reshapeTxDb(txdb,disjoin=TRUE,with.junctions=TRUE,probelen,ignore.strand=TRUE,junction.overlap=5L,exclude.non.std=TRUE,exclude.mir=TRUE,what=c('exon','cds'),mcpar,verbose=FALSE,test.genes)

Arguments

txdb	An object of class TranscriptDb.
disjoin	Logical. Create disjoint exons ranges
with.junctions	Logical. Add 'biological junctions'
probelen	Reads length
ignore.strand	Logical. Ignore strand information
junction.overlap	Minimum overlap of a read with either exons for a junction read in order to be counted
exclude.non.std	Logical. Shall the 'non standard' chromosomes be removed?
exclude.mir	Logical. Remove microRNAs
what	What kind of exons to take into account. General "exons" or "cds"
mcpar	An object of (virtual) class "BiocParallelParam" specifying parameters for parallel computing using BiocParallel
verbose	Logical. Print information during computation
test.genes	Character vector. Subset of gene names to consider. Basically for debugging.

Value

A GRangesList containing GRanges for each gene

Author(s)

Stefano Calza <[e-mail]>, Chen Suo, Agus Salim and Yudi Pawitan

References

Suo C, Calza S, Salim A, Pawitan Y. Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data. Bioinformatics. 2014 Feb 15;30(4):506-13

See Also

makeTranscriptDb, exonsBy

Examples

## Not run: 

seqs <- seqnames(seqinfo(TxDb.Hsapiens.UCSC.hg19.knownGene))
sel <- rep(FALSE,length(seqs))
names(sel) <- seqs
sel["chr14"] <- TRUE
isActiveSeq(TxDb.Hsapiens.UCSC.hg19.knownGene) <- sel

library(TxDb.Hsapiens.UCSC.hg19.knownGene)

param = SerialParam()

txdb <- reshapeTxDb(TxDb.Hsapiens.UCSC.hg19.knownGene,probelen = 50L,mcpar=param)


## End(Not run)

Senbee/Sequgio documentation built on May 9, 2019, 1:21 p.m.