genFeatures: Generate feature ranges from TxDb

In tgirke/systemPipeR: systemPipeR: Workflow Environment for Data Analysis and Report Generation

Generate feature ranges from TxDb

Description

Function to generate a variety of feature types from TxDb objects using utilities provided by the GenomicFeatures package. The feature types are organized per gene and can be returned on that level in their non-reduced or reduced form.

Currently, supported features include intergenic, promoter, intron, exon, cds, 5'/3'UTR and different transcript types. The latter contains as many transcript types as available in the tx_type column when extracting transcripts from TxDb objects as follows: transcripts(txdb, c("tx_name", "gene_id", "tx_type"))

Usage

genFeatures(txdb, featuretype = "all", reduce_ranges, upstream = 1000, downstream = 0, verbose = TRUE)

Arguments

txdb	TxDb object
featuretype	Feature types can be specified by assigning a character vector containing any of the following: c("tx_type", "promoter", "intron", "exon", "cds", "fiveUTR", "threeUTR", "intergenic"). The default all is a shorthand to select all supported features.
reduce_ranges	If set to TRUE the feature ranges will be reduced on the gene level. As a result overlapping feature components of the same type and from the same gene will be merged to a single range, e.g. two overlapping exons from the same gene are merged to one. Intergenic ranges are not affected by this setting. Note, all reduced feature types are labeled with the suffix '_red'.
upstream	Defines for promoter features the number of bases upstream from the transcription start site.
downstream	Defines for promoter features the number of bases downstream from the transcription start site.
verbose	verbose=FALSE turns off all print messages.

Value

The results are returned as a GRangesList where each component is a GRanges object containing the range set of each feature type. Intergenic ranges are assigned unique identifiers and recorded in the featuretype_id column of the metadata block. For this the ids of their adjacent genes are concatenated with two underscores as separator. If the adjacent genes overlap with other genes then their identifiers are included in the id string as well and separated by a single underscore.

Author(s)

Thomas Girke

See Also

transcripts and associated TxDb accessor functions from the GenomicFeatures package.

Examples

## Sample from txdbmaker package
library(txdbmaker)
gffFile <- system.file("extdata", "GFF3_files", "a.gff3", package="txdbmaker")
txdb <- makeTxDbFromGFF(file=gffFile, format="gff3", organism="Solanum lycopersicum")
feat <- genFeatures(txdb, featuretype="all", reduce_ranges=FALSE, upstream=1000, downstream=0)

## List extracted feature types
names(feat)

## Obtain feature lists by genes, here for promoter
split(feat$promoter, unlist(mcols(feat$promoter)$feature_by))

## Return all features in single GRanges object
unlist(feat)

## Not run: 
## Sample from systemPipeRdata package
file <- system.file("extdata/annotation", "tair10.gff", package="systemPipeRdata")
txdb <- makeTxDbFromGFF(file=file, format="gff3", organism="Arabidopsis")
feat <- genFeatures(txdb, featuretype="all", reduce_ranges=TRUE, upstream=1000, downstream=0)

## End(Not run)

tgirke/systemPipeR documentation built on Sept. 24, 2024, 9:48 a.m.