cell_type_DE: Test differential expression of isoforms across cell types
In ConesaLab/acorde: Isoform co-usage networks from single-cell RNA-seq data

cell_type_DE

R Documentation

Test differential expression of isoforms across cell types

Description

This function provides a wrapper to compute Differential Expression across multiple cell types on a single-cell dataset, using standard bulk tools edgeR and DESeq2 and ZINBWaVE weights, as described by Van den Berge et al. (see references below).

Usage

cell_type_DE(
  data,
  mode = c("edgeR", "DESeq2", "both"),
  compute_weights = TRUE,
  AdjPvalue = NULL,
  maxFC = NULL,
  offset = NULL
)

Arguments

`data`	A `SingleCellExperiment` (SCE) object including isoform-level counts on the `assay()` slot and a `cell_type` column indicating cell type correspondence in the `colData()` slot.
`mode`	A character value indicating whether `"edgeR"`, `"DESeq2"` or `"both"` DE methods are to be run.
`compute_weights`	A logical value. If `TRUE`, cell-level weights will be computed using ZINBWaVE (see `zinbwave`). Alternatively, weights may be pre-computed and stored in the `weights()` slot in the SCE object.
`AdjPvalue`	A numeric value. If provided, filtering of DE results by adjusted p-value is enabled.
`maxFC`	A numeric value. If provided, filtering of DE results by maximum fold-change (maxFC) across cell types is enabled. Note that FC filter is based on edgeR's output (FC between all conditions), and therefore this option requires modes `"edgeR"` or `"both"` to be enabled.
`offset`	Optionally, a matrix containing offset information to be considered for bias correction in edgeR and/or DESeq2 DE tests.

Value

If mode = "both", a named list of length 2 containing the results (filtered or not, depending on whether AdjPvalue and maxFC are provided) of testing Differential Expression using edgeR and DESeq2. If maxFC is provided, columns max_FC and max_log2FC are added to the results tables. If the mode argument was used to select only one method, the function returns a data.frame object containing the results table obtained by that method.