major_features: Extract major features from the annotation file

In irilenia/baerhunter: Detection and Analysis of Expressed Intergenic Elements in Bacterial RNA-seq Data

Extract major features from the annotation file

Description

The function extracts parent features only; it also excludes all non-coding RNAs that are already annotated in the file.

Usage

major_features(
  annotation_file,
  annot_file_directory = ".",
  target_strand,
  original_sRNA_annotation
)

Arguments

annotation_file	GFF3 genome annotation file.
annot_file_directory	The directory path for the annotation file (default is '.')
target_strand	A character string indicating the strand. Supports two valies; '+' and '-'.
original_sRNA_annotation	A string indicating how the biotype of pre-annotated ncRNA, which can be found in the attribute column.In case if the user does not know how the sRNA is annotated, it can be set as "unknown". In this case, all RNAs apart from tRNAs and rRNAs will be removed from the selection.

Value

A dataframe with the major features from a set strand.

irilenia/baerhunter documentation built on May 18, 2024, 11:56 p.m.