zentutils: ZentUtils Constructor Function

In gzentner/ZentUtils: Miscellaneous Tools for Sequence Analysis

Description

Creates a new ZentUtils object that stores a GRanges object generated from an imported BED file.

Usage

zentutils(data, genome = NA, mito_chr = "chrM")

Arguments

data	A BED file containing the regions of interest.
genome	Identifier for the genome from which the regions were derived.
mito_chr	Seqname of mitochondrial chromosome.

Details

• The BED file should contain 6 columns, with chromosome, start, and end coordinates in columns 1-3 and strand in column 6.

• BED columns names are converted to "seqnames", "start", "end", "region_name", "score", and "strand" upon import.

Value

A new ZentUtils object with a GRanges object in the 'regions' slot.

Examples

zent <- zentutils(system.file("extdata", "homer_reb1_badis_motif_scan.bed", package = "ZentUtils"), genome = "sacCer3", mito_chr = "chrM")

gzentner/ZentUtils documentation built on June 16, 2021, 12:24 a.m.