.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.
.formatDEAList( inSCE, useAssay, index1 = NULL, index2 = NULL, class = NULL, classGroup1 = NULL, classGroup2 = NULL, groupName1, groupName2, analysisName, covariates = NULL, overwrite = FALSE )
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 |
index2 |
Any type of indices that can subset a
SingleCellExperiment inherited object by cells. specifies
the control group against those specified by |
class |
A vector/factor with |
classGroup1 |
a vector specifying which "levels" given in |
classGroup2 |
a vector specifying which "levels" given in |
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 |
overwrite |
A logical scalar. Whether to overwrite result if exists.
Default |
A list object with part of formatted DE analysis information
Yichen Wang