Guitar (version 1.10.0)

makeGuitarCoordsFromTxDb: makeGuitarCoordsFromTxDb

Description

Make a Guitar Coordinates from TranscriptDb object, i.e., making Guitar coordinates for 8 different components, including, 5'UTR, CDS, 3'UTR, lncRNA, Pomoter and Tail of mRNA and lncRNA. Additional filters will discard transcripts that are too short or has too much ambigous on Genome to increase the sensitivity of the analysis.

Usage

makeGuitarCoordsFromTxDb(txdb, maximalAmbiguity = 3,  minimalComponentLength = 100, minimalNcRNALength = 300,  noBins = 100)

Arguments

txdb

A transcriptDb object, which can be generated from makeTxDbFromUCSC or other functions.

maximalAmbiguity

If a transcript overlap with more number of transcripts than this number, this transcript will be used in the analysis. By filtering out a number of transcripts, this filter also decrease memory usage and computation time. Default: 3.

minimalComponentLength

The mimimal length of the components (5'UTR, CDS, 3'UTR) of a mRNA. Unfortunately, some mRNAs do not all 3 components or some components can be too short and cannot provide effective resolution for the analysis. These mRNAs will be filtered out from the analysis. Default: 100

minimalNcRNALength

non-coding RNAs with length smaller than this value will not be used in the analysis.

noBins

The number of sections the "transcript" of the GRangesList object will be equally divided into. This is the resolution of the Guitar coordinates. The larger noBins is, the clearer the visualization will be; however, more computation time and memory resource will be required. You may want to set a smaller number when using a slow computer. Default: 100.

Value

A Guitar coordiantes (GRanges object) will be returned, with Transcript ID, the relative position of each GRanges on the RNA transcript, the interval (bp) between different coordiantes on a transcript component: Front (DNA), Back (DNA), 5'UTR, CDS, 3'UTR, lncRNA.

Examples

txdb_file <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                         package="GenomicFeatures")
txdb <- loadDb(txdb_file)
gc_txdb <- makeGuitarCoordsFromTxDb(txdb,noBins =3)
gc_txdb