seg2gr: Convert GRanges-like data.frame into GRanges

In mskilab/gUtils: R Package Providing Additional Capabilities and Speed for GenomicRanges Operations

Convert GRanges-like data.frame into GRanges

Description

Input data.frame of segments "segs" and converts into GRanges object porting over additional value columns

"segs" data.frame/data.table can obey any number of conventions to specify chrom, start, and end of ranges (e.g. $pos1, $pos2, $Start_position, $End_position)

Please see documentation for function 'standardize_segs()' for more details.

Usage

seg2gr(segs, seqlengths = NULL, seqinfo = Seqinfo())

Arguments

segs	data.frame (or data.table) of segments with fields denoting chromosome, start, end, and other metadata. (See function 'standardize_segs()' for 'seg' data.frame/data.table input formats)
seqlengths	seqlengths of output GRanges object (default = NULL)
seqinfo	seqinfo of output GRanges object (default = Seqinfo())

Value

GRanges from converted "segs" data.frame/data.table

mskilab/gUtils documentation built on June 6, 2023, 12:08 a.m.