Set differential expression options

Change options of the differential expression analysis (only those given); nothing runs.

Usage

cellucid_analysis_differential_set(viewer, options, in_ = "panel", show = FALSE)

Arguments

viewer

A viewer cellucid_view() or cellucid_serve() returned.

options

A named list. Required.

categoriesB

Group B: all, or the categories (or pages) by name. Either a named list; or a named list. Optional.

ids

A vector or list of text (at least 1 character) (each once). Required.

compare

Compare. One of "pages", "categories". Optional.

correction

Multiple testing. One of "bh", "bonferroni". Optional.

excludeGenes

Exclude genes. A vector or list of text (each once). Optional.

excludePattern

Exclude pattern. Text. Optional.

field

Field. Text. Optional.

foldChange

Fold change from. One of "auto", "log1p", "stored". Optional.

labels

Labelled genes. A whole number (at least 0). Optional.

matrix

Expression matrix. Text. Optional.

maxAdjP

Max adjusted p. A number (at least 0, at most 1). Optional.

method

Method. One of "wilcox", "ttest", "ttest_overestim_var". Optional.

minCells

Min cells per group. A whole number (at least 2). Optional.

minCellsPerSample

Min cells per sample. A whole number (at least 1). Optional.

minLog2FC

Min |log2FC|. A number (at least 0). Optional.

minPct

Min % expressing in either group. A number (at least 0, at most 100). Optional.

onlyGenes

Only genes in. Text. Optional.

onlyGenesList

Gene list. Text. Optional.

pConvention

Wilcoxon p-values. One of "exact", "normal", "normal_tie". Optional.

pageA

Group A. Text. Optional.

pageB

Group B. Text. Optional.

replicates

Replicates. Text. Optional.

within

Within. Text. Optional.

withinCategories

Within categories: all, or the categories (or pages) by name. Either a named list; or a named list. Optional.

ids

A vector or list of text (at least 1 character) (each once). Required.

withinField

Within field. Text. Optional.

in_

Either exactly "panel" (The Analysis panel); or a whole number (at least 1) (A floating analysis window, by its number (1 is the first open)). Default "panel", the viewer's own. Sent as the parameter in.

show

Also open it in the Analysis panel (with in "panel"), as another analysis's "send to" does. TRUE or FALSE. Default FALSE, the viewer's own.

Value

A cellucid_action_request, at once and invisibly: the action is sent now, or when the viewer's channel opens. cellucid_action_result(request) returns its outcome (what it did, as names, counts and ids), or NULL when it had nothing to report; request$step is the history step it made.

Details

The viewer's action analysis.differential.set (Analysis). It changes the viewer's state: one step of the viewer's history, labelled as R's, undone like any other. The state it can change: analysis.

See also

cellucid_act() sends any action by its type, and cellucid_action_result() collects its answer.

Examples

if (interactive() && requireNamespace("SeuratObject", quietly = TRUE)) {
  data("pbmc_small", package = "SeuratObject")
  viewer <- cellucid_view(SeuratObject::UpdateSeuratObject(pbmc_small))
  request <- cellucid_analysis_differential_set(viewer,
      options = list())
  print(request)
  # cellucid_action_result(request) waits for its outcome.
  cellucid_stop(viewer)
}