ExploratorySummarizedExperiment: ExploratorySummarizedExperiments

In pinin4fjords/shinyngs: Shiny apps for NGS data

ExploratorySummarizedExperiments

Description

This function creates objects of the ExploratorySummarizedExperiment class, an extension of SummarizedExperiment designed to hold additional information about the features present - for example differential expression values and the type of identifiers used in rows.

Usage

ExploratorySummarizedExperiment(
  assays,
  colData,
  annotation,
  idfield,
  labelfield = character(),
  entrezgenefield = character(),
  contrast_stats = list(),
  assay_measures = list(),
  gene_set_analyses = list(),
  dexseq_results = list(),
  read_reports = list()
)

Arguments

assays	An object of class SimpleList as would be supplied to the SummarizedExperiment constructor
colData	An object of class DataFrame as would be supplied to the SummarizedExperimentConstructor. Row names could correspond to column names in the matrices in assays
annotation	A data frame with annotation for the features (rows) of the assays matrices. Rows must correspond to to those matrices.
idfield	To which of the annotation columns do row names correspond?
labelfield	Which column from annotation should be used to label features (e.g. a gene name field)?
entrezgenefield	Which column from annotation is the Entrez gene ID?
contrast_stats	List of matrices containing contrast-related statistics. Only 'pvals', 'qvals' and 'fold_changes' are currently used. Fold changes are calculated on the fly where not supplied. Matrix columns correspond to 'contrasts' set in the containing SummarizedExperimentList.
assay_measures	Optional List of measures to display related to each assay.
gene_set_analyses	List of lists of gene set tables keyed first by gene set type and secondly by contrast
dexseq_results	An optional list of DEXSeqResults objects corresponding to the contrasts listed in the contrasts slot..
read_reports	A named list of matrices with read counts in columns and sample names in rows. Useful for providing mapped read counts, counts per gene type etc

Details

It is intended that one or more ExploratorySummarizedExperiments with the same samples (columns) are contained within an ExploratorySumarizedExperimentList, which will contain information relevant to all experiments such as gene sets and contrasts.

It's clear that the structure of this class and that of SummarizedExperimentList will need to be refined in future.

Value

output An ExploratoryRangedSummarizedExperient object

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