ExploratorySummarizedExperimentLists, containers for ExploratorySummarizedExperiments

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 list of named lists of character vectors of gene identifiers, as produced by reading .gmt format gene sets (for example from MSigDB) with read_gmt. 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 pick an igv.js genome build for the gene model view in the gene module (see geneModelGenomeInfo()).

Value

output An ExploratorySummarizedExperimentList

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

Examples

data(airway, package = "airway")
ese <- as(airway, "ExploratorySummarizedExperiment")
eselist <- ExploratorySummarizedExperimentList(ese, title = "Airway study")
#> Creating ExploratorySummarizedExperimentList object