ExploratorySummarizedExperimentList: ExploratorySummarizedExperimentLists, containers for...

In pinin4fjords/shinyngs: Shiny apps for NGS data

ExploratorySummarizedExperimentLists, containers for ExploratorySummarizedExperiments

Description

ExploratorySummarizedExperiment lists are intented to contain one or more ExploratorysummarizedExperiments with the same sets of samples/columns but different feature sets. The motivating use case was the desire to examine expression at both transcript and gene levels in RNA-seq experiments explorted via Shinyngs

Usage

ExploratorySummarizedExperimentList(
  eses,
  title = "",
  author = "",
  description = "",
  static_pdf = character(),
  group_vars = character(),
  default_groupvar = character(),
  contrasts = list(),
  url_roots = list(),
  gene_sets = list(),
  gene_set_id_type = character(),
  ensembl_species = character()
)

Arguments

eses	List of ExploratorySummarizedExperiments
title	Study title
author	Study authors
description	Study summary to displayed on front page
static_pdf	A URL to a static PDF document to be displayed on the front page.
group_vars	Variables by which a user will be allowed to group the samples of individual experiments, must correspond to their colData
default_groupvar	Default group_var
contrasts	List of length-3 vectors containing 1) the group_var, 2) the group_var value corresponding to the 'control' side and 3) the value corresponding to the 'treatment' side
url_roots	A list of URL roots, with list names corresponding to metadata column names of the experiments. Exploratory tools displayed via shinyngs can use these roots to construct URLs to 'link out'.
gene_sets	A named list of GeneSetCollections as might be produced by reading .gmt format gene sets (for example from MSigDB) using GSEABase::getGmt(). These must contain identifiers of the type specified in gene_set_id_type.
gene_set_id_type	A column found in the metadata of the component ExploratorySummarizedExperiment objects via mcols(). Used to relate the rows of assays to gene sets.
ensembl_species	Ensembl species definition like 'mmusculus'. Used to interface with BiomaRt e.g. to make gene model plots in the gene module.

Details

As a the containing object for experiments, this class is intented to contain various variables relevant across a whole study, which will be displayed in an exploratory interface generated in shinyngs. This includes the study title, author etc as well as definitions of the contrasts used in differential analysis and the gene sets relevant to all experiments

Value

output An ExploratorySummarizedExperimentList

pinin4fjords/shinyngs documentation built on Jan. 18, 2025, 7:09 p.m.