runDEAnalysis: Perform differential expression analysis on SCE object

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

Perform differential expression analysis on SCE object

Description

Perform differential expression analysis on SCE object

Usage

runDEAnalysis(inSCE, method = "wilcox", ...)

runDESeq2(
  inSCE,
  useAssay = "counts",
  useReducedDim = NULL,
  index1 = NULL,
  index2 = NULL,
  class = NULL,
  classGroup1 = NULL,
  classGroup2 = NULL,
  analysisName,
  groupName1,
  groupName2,
  covariates = NULL,
  fullReduced = TRUE,
  onlyPos = FALSE,
  log2fcThreshold = NULL,
  fdrThreshold = NULL,
  minGroup1MeanExp = NULL,
  maxGroup2MeanExp = NULL,
  minGroup1ExprPerc = NULL,
  maxGroup2ExprPerc = NULL,
  overwrite = FALSE,
  verbose = TRUE
)

runLimmaDE(
  inSCE,
  useAssay = "logcounts",
  useReducedDim = NULL,
  index1 = NULL,
  index2 = NULL,
  class = NULL,
  classGroup1 = NULL,
  classGroup2 = NULL,
  analysisName,
  groupName1,
  groupName2,
  covariates = NULL,
  onlyPos = FALSE,
  log2fcThreshold = NULL,
  fdrThreshold = NULL,
  minGroup1MeanExp = NULL,
  maxGroup2MeanExp = NULL,
  minGroup1ExprPerc = NULL,
  maxGroup2ExprPerc = NULL,
  overwrite = FALSE,
  verbose = TRUE
)

runANOVA(
  inSCE,
  useAssay = "logcounts",
  useReducedDim = NULL,
  index1 = NULL,
  index2 = NULL,
  class = NULL,
  classGroup1 = NULL,
  classGroup2 = NULL,
  analysisName,
  groupName1,
  groupName2,
  covariates = NULL,
  onlyPos = FALSE,
  log2fcThreshold = NULL,
  fdrThreshold = NULL,
  minGroup1MeanExp = NULL,
  maxGroup2MeanExp = NULL,
  minGroup1ExprPerc = NULL,
  maxGroup2ExprPerc = NULL,
  overwrite = FALSE,
  verbose = TRUE
)

runMAST(
  inSCE,
  useAssay = "logcounts",
  useReducedDim = NULL,
  index1 = NULL,
  index2 = NULL,
  class = NULL,
  classGroup1 = NULL,
  classGroup2 = NULL,
  analysisName,
  groupName1,
  groupName2,
  covariates = NULL,
  onlyPos = FALSE,
  log2fcThreshold = NULL,
  fdrThreshold = NULL,
  minGroup1MeanExp = NULL,
  maxGroup2MeanExp = NULL,
  minGroup1ExprPerc = NULL,
  maxGroup2ExprPerc = NULL,
  overwrite = FALSE,
  check_sanity = TRUE,
  verbose = TRUE
)

runWilcox(
  inSCE,
  useAssay = "logcounts",
  useReducedDim = NULL,
  index1 = NULL,
  index2 = NULL,
  class = "cluster",
  classGroup1 = c(1),
  classGroup2 = c(2),
  analysisName = "cluster1_VS_2",
  groupName1 = "cluster1",
  groupName2 = "cluster2",
  covariates = NULL,
  onlyPos = FALSE,
  log2fcThreshold = NULL,
  fdrThreshold = NULL,
  minGroup1MeanExp = NULL,
  maxGroup2MeanExp = NULL,
  minGroup1ExprPerc = NULL,
  maxGroup2ExprPerc = NULL,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

inSCE	SingleCellExperiment inherited object.
method	Character. Specify which method to use when using runDEAnalysis(). Choose from "wilcox", "MAST", "DESeq2", "Limma", "ANOVA". Default "wilcox".
...	Arguments to pass to specific methods when using the generic runDEAnalysis().
useAssay	character. A string specifying which assay to use for the DE regression. Ignored when useReducedDim is specified. Default "counts" for DESeq2, "logcounts" for other methods.
useReducedDim	character. A string specifying which reducedDim to use for DE analysis. Will treat the dimensions as features. Default NULL.
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 "cluster".
classGroup1	a vector specifying which "levels" given in class are of interests. Default c(1).
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. Default c(2).
analysisName	A character scalar naming the DEG analysis. Default "cluster1_VS_2".
groupName1	A character scalar naming the group of interests. Default "cluster1".
groupName2	A character scalar naming the control group. Default "cluster2".
covariates	A character vector of additional covariates to use when building the model. All covariates must exist in names(colData(inSCE)). Default NULL.
fullReduced	Logical, DESeq2 only argument. Whether to apply LRT (Likelihood ratio test) with a 'full' model. Default TRUE.
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 NULL.
fdrThreshold	Only out put DEGs with FDR value less than this value. Default NULL.
minGroup1MeanExp	Only out put DEGs with mean expression in group1 greater then this value. Default NULL.
maxGroup2MeanExp	Only out put DEGs with mean expression in group2 less then this value. Default NULL.
minGroup1ExprPerc	Only out put DEGs expressed in greater then this fraction of cells in group1. Default NULL.
maxGroup2ExprPerc	Only out put DEGs expressed in less then this fraction of cells in group2. Default NULL.
overwrite	A logical scalar. Whether to overwrite result if exists. Default FALSE.
verbose	A logical scalar. Whether to show messages. Default TRUE.
check_sanity	Logical, MAST only argument. Whether to perform MAST's sanity check to see if the counts are logged. Default TRUE.

Details

SCTK provides Limma, MAST, DESeq2, ANOVA and Wilcoxon test for differential expression analysis, where DESeq2 expects non-negtive integer assay input while others expect logcounts.

Condition specification allows two methods: 1. Index level selection. Only use arguments index1 and index2. 2. Annotation level selection. Only use arguments class, classGroup1 and classGroup2.

Value

The input SingleCellExperiment object, where metadata(inSCE)$diffExp is updated with a list named by analysisName, with elements of:

$groupNames	the naming of the two conditions
$useAssay, $useReducedDim	the matrix name that was used for calculation
$select	the cell selection indices (logical) for each condition
$result	a data.frame of the DEGs table
$method	the method used

See Also

See plotDEGHeatmap, plotDEGRegression, plotDEGViolin and plotDEGVolcano for visualization method after running DE analysis.

Examples

data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- scaterlogNormCounts(sce, assayName = "logcounts")
sce <- runDEAnalysis(method = "Limma", inSCE = sce, groupName1 = "group1",
 groupName2 = "group2", index1 = seq(20), index2 = seq(21,40),
 analysisName = "Limma")

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.