Find_Markers: Find_Markers

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

Find_Markers

Description

Find_Markers

Usage

Find_Markers(
  seuratObj,
  identFields,
  outFile = NULL,
  testsToUse = c("wilcox", "MAST", "DESeq2"),
  numGenesToPrint = 20,
  onlyPos = F,
  pValThreshold = 0.001,
  foldChangeThreshold = 0.5,
  minPct = 0.1,
  minDiffPct = -Inf,
  datasetName = NULL,
  assayName = "RNA",
  verbose = FALSE,
  doPairwise = FALSE
)

Arguments

seuratObj	A seurat object
identFields	A vector of grouping fields for DE. Often these are the resolution, computed during FindClustersAndDimRedux()
outFile	A file where a table of markers will be saved
testsToUse	A vector of tests to be used. Each will be used to run FindAllMarkers() and the results merged. Available are: wilcox, bimod, roc, t, negbinom, poisson, LR, MAST, DESeq2
numGenesToPrint	The number of top markers per cluster to print in a table
onlyPos	If true, only positive markers will be saved
pValThreshold	Only genes with adjusted p-values below this will be reported
foldChangeThreshold	Only genes with log2 fold-change above this will be reported
minPct	Only test genes that are detected in a minimum fraction of min.pct cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed.
minDiffPct	Only test genes that show a minimum difference in the fraction of detection between the two groups.
datasetName	An optional label for this dataset. If provided, this will be appended to the resulting table.
assayName	The assay to use.
verbose	Passed to Seurat::FindMarkers
doPairwise	If true, rather than use Seurat::FindAllMarkers, the code will iterate each pair of values and generate a list of DEGs from these comparisons. This can help identify markers highly differentially expressed between some groups, but shared between others.

Value

A DT::datatable object with the top markers, suitable for printing

bimberlabinternal/CellMembrane documentation built on Dec. 20, 2024, 11:13 p.m.