geneGRanges: Given a GenomicFeatures annotation_db and a gene_id, extract...

In BrentLab/brentlabRnaSeqTools: Management/QC for brentlab RNAseq data

Given a GenomicFeatures annotation_db and a gene_id, extract an GRanges object of the cds

Description

Given a GenomicFeatures annotation_db and a gene_id, extract an GRanges object of the cds

Usage

geneGRanges(
  annote_obj_path,
  gene_id,
  id_col = "ID",
  feature_col = "type",
  feature = "cds"
)

Arguments

annote_obj_path	path to an annotation file parsed by rtracklayer::import
gene_id	the ID of a gene in the db. Eg, for cryptococcus CKF44_05222
id_col	gene feature column. Default is 'ID'
feature_col	feature (col 3) column of annote_obj. Default is 'type'
feature	what feature to select. Default is 'cds'

Value

an IRanges object of a given feature (eg, a gene's cds features)

References

rtracklayer::import

BrentLab/brentlabRnaSeqTools documentation built on Aug. 20, 2023, 9:22 a.m.