seqNdisplayRSession: seq'N'display'R Session

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

seq'N'display'R Session

Description

Container for seqNdisplayR session information

Usage

seqNdisplayRSession(
  df = NULL,
  samples = NULL,
  colors = NULL,
  bigwig_dirs = NULL,
  bigwigs = NULL,
  parameters = NULL,
  annotations = NULL,
  options = NULL,
  load_annotations = F
)

Arguments

df	an optional df, overrides all other options except annotations
samples	samples object as used by seqNdisplay
colors	colors object as used by seqNdisplay
bigwig_dirs	bigwig_dirs object as used by seqNdisplay
bigwigs	bigwigs object as used by seqNdisplay
parameters	parameters object as used by seqNdisplay
annotations	annotations object as used by seqNdisplay
options	named list of other arguments used by seqNdisplay function
load_annotations	load annotations as GRanges? default=FALSE

Details

seqNdisplayR session object holding above slots identical to parameters for seqNdisplay. If df is provided parses information from columns, colors, bigwig_file, bigwig_directory, dataset and subgroup_1, subgroup_2 etc. See Excel template sheet in system.file('extdata','example_excel_template.xls', package='seqNdisplayR') for more information. The df here is tidy, ie all "empty" slots are filled. Otherwise see vignette(package='seqNdisplayR'). If options are not provided, adds default options to session object. If load_annotations=TRUE will try to load annotations using import. OBS: Currently only bed files are used correctly by seqNdisplayR.

Value

Object of class seqNdisplayRSession, which is a named list with slots samples, colors, bigwig_dirs, bigwigs, parameters and annotation_files and annots. Annots is either identical to annotation_files or a named list of loaded GRanges.

Author(s)

MS (minor additions by SLA)

Examples

xl_fname = system.file('extdata', 'sNdR_sample_example_elaborate.xlsx', package='seqNdisplayR')
session <- LoadExcel(xl_fname, load_annotations = T) # takes some time, since annotations are loaded...
feat = 'LMO4'
plot(session, feature=feat)

THJlab/seqNdisplayR documentation built on March 29, 2024, 1:36 p.m.