Get a data frame of intron counts per gene

Usage

get_intron_counts(txdb)

Arguments

txdb: A TxDb object with transcript annotations. See details below for examples on how to create TxDb objects from different kinds of input.

Value

A data frame with intron counts per gene, with variables:

gene: Character with gene IDs.
introns: Numeric with number of introns per gene.

Details

The family of functions makeTxDbFrom* from the txdbmaker package can be used to create TxDb objects from a variety of input data types. You can create TxDb objects from e.g., GRanges objects (makeTxDbFromGRanges()), GFF files (makeTxDbFromGFF()), an Ensembl database (makeTxDbFromEnsembl), and a Biomart database (makeTxDbFromBiomart).

Examples

data(yeast_annot)

# Create TxDb object from GRanges
library(txdbmaker)
txdb <- txdbmaker::makeTxDbFromGRanges(yeast_annot[[1]])
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead

# Get intron counts
intron_counts <- get_intron_counts(txdb)