Perform differential expression analysis on SCE with Limma.

Condition specification allows two methods: 1. Index level selection. Arguments index1 and index2 will be used. 2. Annotation level selection. Arguments class, classGroup1 and classGroup2 will be used.

runLimmaDE(
  inSCE,
  useAssay = "logcounts",
  index1 = NULL,
  index2 = NULL,
  class = NULL,
  classGroup1 = NULL,
  classGroup2 = NULL,
  analysisName,
  groupName1,
  groupName2,
  covariates = NULL,
  onlyPos = FALSE,
  log2fcThreshold = 0.25,
  fdrThreshold = 0.05,
  overwrite = FALSE
)

Arguments

inSCE	SingleCellExperiment inherited object.
useAssay	character. A string specifying which assay to use for the Limma regression. The assay should be a log-transformed normalized assay. Default `"logcounts"`.
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.
analysisName	A character scalar naming the DEG analysis. Required
groupName1	A character scalar naming the group of interests. Required.
groupName2	A character scalar naming the control group. Required.
covariates	A character vector of additional covariates to use when building the model. All covariates must exist in `names(colData(inSCE))`. Default `NULL`.
onlyPos	Whether to only output DEG with positive log2_FC value. Default `FALSE`.
log2fcThreshold	Only out put DEGs with the absolute values of log2FC greater than this value. Default `0.25`
fdrThreshold	Only out put DEGs with FDR value less than this value. Default `0.05`
overwrite	A logical scalar. Whether to overwrite result if exists. Default `FALSE`.

Value

The input SingleCellExperiment object with metadata(inSCE)$diffExp updated with the results: a list named by analysisName, with $groupNames containing the naming of the two conditions, $useAssay storing the assay name that was used for calculation, $select storing the cell selection indices (logical) for each condition, $result storing a data.frame of the DEGs summary, and $method storing "Limma".

Examples

data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- scaterlogNormCounts(sce, assayName = "logcounts")
sce <- runLimmaDE(inSCE = sce, groupName1 = "Sample1",
 groupName2 = "Sample2", index1 = seq(20), index2 = seq(21,40),
 analysisName = "Limma")