extract_lengths: Take gene/exon lengths from a suitable data source...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Take gene/exon lengths from a suitable data source (gff/TxDb/OrganismDbi)

Description

Primarily goseq, but also other tools on occasion require a set of gene IDs and lengths. This function is resposible for pulling that data from either a gff, or TxDb/OrganismDbi.

Usage

extract_lengths(
  db = NULL,
  gene_list = NULL,
  type = "GenomicFeatures::transcripts",
  id = "TXID",
  possible_types = c("GenomicFeatures::genes", "GenomicFeatures::cds",
    "GenomicFeatures::transcripts"),
  ...
)

Arguments

db	Object containing data, if it is a string then a filename is assumed to a gff file.
gene_list	Set of genes to query.
type	Function name used for extracting data from TxDb objects.
id	Column from the resulting data structure to extract gene IDs.
possible_types	Character list of types I have previously used.
...	More arguments are passed to arglist.

Value

Dataframe containing 2 columns: ID, length

See Also

[GenomicFeatures]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.