genFeatures: Generate feature ranges from TxDb
In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description Usage Arguments Value Author(s) See Also Examples

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"))

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

`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.

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.

Thomas Girke

transcripts and associated TxDb accessor functions from the GenomicFeatures package.

## Sample from GenomicFeatures package
library(GenomicFeatures)
gffFile <- system.file("extdata", "GFF3_files", "a.gff3", package="GenomicFeatures")
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=FALSE, upstream=1000, downstream=0)

## End(Not run)