RegionGRanges: Region GRanges

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

Region GRanges

Description

Internal function: Convert feature name or locus to be plotted to a GRanges object

Usage

RegionGRanges(
  locus,
  tracks_width,
  feature = NULL,
  annotations = NULL,
  bin_start = NULL,
  extra_space = c(0.1, 0.1),
  verbosity,
  interface
)

Arguments

locus	genomic coordinates, incl. strand, of locus (e.g., c("chr1", "+", 87297784, 87379607)
tracks_width	width of plotted data tracks in cm
feature	the name of a genomic locus (e.g., LMO4; the name needs to be present within the name column of the provided annotations, which will be searched in the given order).
annotations	named list of GRanges objects representing annotations (produced by ReadInAnnotations)
bin_start	Center the bins around the given genomic position. Provide an integer value that lies within the plotted region. Per default the bin center will be at the 5'-end of the plotted region if it is defined by genomic coordinates and at the 5'-end of the locus if the plotted region is defined by locus name
extra_space	Extra space up- and downstream of and relative to the selected genomic feature (0.1 = 10 percent). Only taken into account when genomic locus (feature) name is entered - ignored when genomic coordinates are entered. Numeric vector - default c(1.0,1.0).
verbosity	indicated by an integer 0 to 3 referring to the levels 'off', 'no warnings', 'normal', and 'detailed'
interface	'R' or 'shiny'

Value

a GRanges object with user-supplied locus coordinates (two metadata columns included with bin_start and tracks_width)

Note

bin_start indicates the coordinate from where binning is centered

tracks_width is the plotted width in cm

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)       
locus_gr = RegionGRanges(locus=NULL, tracks_width=12, feature='LMO4', annotations=annots_listedGR, bin_start=NULL, extra_space=c(0.1,0.1), verbosity=3, interface='R')
locus_gr = RegionGRanges(locus=c('chr1', '+', 87326423, 87350968), tracks_width=12, feature=NULL, annotations=NULL, bin_start=NULL, extra_space=c(0.1,0.1), verbosity=3, interface='R')

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