.formatDEAList {singleCellTK} | R Documentation

## Helper function for differential expression analysis methods that accepts multiple ways of conditional subsetting and returns stable index format. Meanwhile it does all the input checkings.

### Description

Helper function for differential expression analysis methods that accepts multiple ways of conditional subsetting and returns stable index format. Meanwhile it does all the input checkings.

### Usage

    .formatDEAList(
      inSCE,
      useAssay,
      index1 = NULL,
      index2 = NULL,
      class = NULL,
      classGroup1 = NULL,
      classGroup2 = NULL,
      groupName1,
      groupName2,
      analysisName,
      covariates = NULL,
      overwrite = FALSE
    )

### Arguments

`inSCE` | SingleCellExperiment inherited object. Required.
`useAssay` | character. A string specifying which assay to use. Required.
`index1` | Any type of indices that can subset a SingleCellExperiment inherited object by cells. Specifies which cells are of interests. Default `NULL`.
`index2` | Any type of indices that can subset a SingleCellExperiment inherited object by cells. specifies the control group against those specified by `index1`. If `NULL` when using index specification, `index1` cells will be compared with all other cells. Default `NULL`.
`class` | A vector/factor with `ncol(inSCE)` elements, or a character scalar that specifies a column name of `colData(inSCE)`. Default `NULL`.
`classGroup1` | a vector specifying which "levels" given in `class` are of interests. Default `NULL`.
`classGroup2` | a vector specifying which "levels" given in `class` is the control group against those specified by `classGroup1`. If `NULL` when using annotation specification, `classGroup1` cells will be compared with all other cells.
`groupName1` | A character scalar naming the group of interests. Required.
`groupName2` | A character scalar naming the control group. Required.
`analysisName` | A character scalar naming the DEG analysis. Required
`covariates` | A character vector of additional covariates used in linear regression methods such as Limma and DESeq2. Default `NULL`
`overwrite` | A logical scalar. Whether to overwrite result if exists. Default `FALSE`.

### Value

A list object with part of formatted DE analysis information

### Author(s)

Yichen Wang

[Package singleCellTK version 2.2.0 Index]