ReadInAnnotations: Read In Annotations

In THJlab/seqNdisplayR: A Tool for Customizable and Reproducible Plotting of Sequencing Coverage Data

Read In Annotations

Description

Internal function: Read in annotations as GRanges objects from bed files - stored in list format

Usage

ReadInAnnotations(annots, verbosity = 3)

Arguments

annots	named list of bed file names (incl. full path; can be stored both locally and on http)
verbosity	indicated by an integer 0 to 3 referring to the levels 'off', 'no warnings', 'normal', and 'detailed'

Value

named list GRanges objects for each given bed file

Note

bed files can be imported from http on both MacOS and Windows (not true for bigwig files on Windows)

Author(s)

SLA

Examples

annots_fnames = list('gencode v21'='http://genome-ftp.mbg.au.dk/public/THJ/seqNdisplayR/examples/annotations/gencode.v21.annotation.nohosted.bed',
                     'in-house'='http://genome-ftp.mbg.au.dk/public/THJ/seqNdisplayR/examples/annotations/HeLa_major_isoform_hg38_gc34.bed')
annots_listedGR = ReadInAnnotations(annots=annots_fnames, verbosity=3)               

THJlab/seqNdisplayR documentation built on Nov. 13, 2024, 10:36 a.m.