ExploratorySummarizedExperiments

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(),
  gene_set_analyses_tool = 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

Three-level nested lists of gene set tables keyed first by assay, then by gene set type and then 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

gene_set_analyses_tool

Three-level nested lists of a string, nested as gene_set_analyses. Each string may be "auto" (the default), "gsea" or "roast". It defines the format of the corresponding gene_set_analyses table.

Value

output An ExploratoryRangedSummarizedExperient object

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.

Examples

expression <- matrix(1:12, nrow = 3,
  dimnames = list(c("ENSG1", "ENSG2", "ENSG3"), paste0("s", 1:4)))
coldata <- data.frame(
  condition = rep(c("treated", "control"), each = 2),
  row.names = paste0("s", 1:4)
)
annotation <- data.frame(
  gene_id = c("ENSG1", "ENSG2", "ENSG3"),
  gene_name = c("GeneA", "GeneB", "GeneC"),
  row.names = c("ENSG1", "ENSG2", "ENSG3")
)
ExploratorySummarizedExperiment(
  assays = list(expression = expression),
  colData = coldata,
  annotation = annotation,
  idfield = "gene_id",
  labelfield = "gene_name"
)
#> class: ExploratorySummarizedExperiment 
#> dim: 3 4 
#> metadata(0):
#> assays(1): expression
#> rownames(3): ENSG1 ENSG2 ENSG3
#> rowData names(2): gene_id gene_name
#> colnames(4): s1 s2 s3 s4
#> colData names(1): condition