dot-formatDEAList: Helper function for differential expression analysis methods...

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

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

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.