resDS {muscat} | R Documentation

## resDS Formatting of DS analysis results

### Description

`resDS` provides a simple wrapper to format cluster-level differential testing results into an easily filterable table, and to optionally append gene expression frequencies by cluster-sample & -group, as well as cluster-sample-wise CPM.

### Usage

    resDS(
      x,
      y,
      bind = c("row", "col"),
      frq = FALSE,
      cpm = FALSE,
      digits = 3,
      sep = "__",
      ...
    )

### Arguments

`x` | a `SingleCellExperiment`.
`y` | a list of DS testing results as returned by `pbDS` or `mmDS`.
`bind` | character string specifying the output format (see details).
`frq` | logical or a pre-computed list of expression frequencies as returned by `calcExprFreqs`.
`cpm` | logical specifying whether CPM by cluster-sample should be appendeded to the output result table(s).
`digits` | integer value specifying the number of significant digits to maintain.
`sep` | character string to use as separator when constructing new column names.
`...` | optional arguments passed to `calcExprFreqs` if `frq = TRUE`.

### Details

When `bind = "col"`, the list of DS testing results at `y$table` will be merge vertically (by column) into a single table in tidy format with column `contrast/coef` specifying the comparison.

Otherwise, when `bind = "row"`, an identifier of the respective contrast or coefficient will be appended to the column names, and all tables will be merge horizontally (by row).

Expression frequencies pre-computed with `calcExprFreqs` may be provided with `frq`. Alternatively, when `frq = TRUE`, expression frequencies can be computed directly, and additional arguments may be passed to `calcExprFreqs` (see examples below).

### Value

returns a 'data.frame'.

### Author(s)

Helena L Crowell & Mark D Robinson

### Examples

    # compute pseudobulks (sum of counts)
    data(example_sce)
    pb <- aggregateData(example_sce,
      assay = "counts", fun = "sum")

    # run DS analysis (edgeR on pseudobulks)
    res <- pbDS(pb, method = "edgeR")

    head(resDS(example_sce, res, bind = "row")) # tidy format
    head(resDS(example_sce, res, bind = "col", digits = Inf))

    # append CPMs & expression frequencies
    head(resDS(example_sce, res, cpm = TRUE))
    head(resDS(example_sce, res, frq = TRUE))

    # pre-computed expression frequencies & append
    frq <- calcExprFreqs(example_sce, assay = "counts", th = 0)
    head(resDS(example_sce, res, frq = frq))

[Package muscat version 1.6.0 Index]