getMarkerFeatures.Rd
This function will identify features that are definitional of each provided cell grouping where possible
getMarkerFeatures( ArchRProj = NULL, groupBy = "Clusters", useGroups = NULL, bgdGroups = NULL, useMatrix = "GeneScoreMatrix", bias = c("TSSEnrichment", "log10(nFrags)"), normBy = NULL, testMethod = "wilcoxon", maxCells = 500, scaleTo = 10^4, threads = getArchRThreads(), k = 100, bufferRatio = 0.8, binarize = FALSE, useSeqnames = NULL, verbose = TRUE, logFile = createLogFile("getMarkerFeatures") )
ArchRProj | An |
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groupBy | The name of the column in |
useGroups | A character vector that is used to select a subset of groups by name from the designated |
bgdGroups | A character vector that is used to select a subset of groups by name from the designated |
useMatrix | The name of the matrix to be used for performing differential analyses. Options include "GeneScoreMatrix", "PeakMatrix", etc. |
bias | A character vector indicating the potential bias variables (i.e. c("TSSEnrichment", "log10(nFrags)")) to account
for in selecting a matched null group for marker feature identification. These should be column names from |
normBy | The name of a numeric column in |
testMethod | The name of the pairwise test method to use in comparing cell groupings to the null cell grouping during marker feature identification. Valid options include "wilcoxon", "ttest", and "binomial". |
maxCells | The maximum number of cells to consider from a single-cell group when performing marker feature identification. |
scaleTo | Each column in the matrix designated by |
threads | The number of threads to be used for parallel computing. |
k | The number of nearby cells to use for selecting a biased-matched background while accounting for |
bufferRatio | When generating optimal biased-matched background groups of cells to determine significance, it can be difficult
to find sufficient numbers of well-matched cells to create a background group made up of an equal number of cells. The |
binarize | A boolean value indicating whether to binarize the matrix prior to differential testing. This is useful when
|
useSeqnames | A character vector that indicates which |
verbose | A boolean value that determines whether standard output is printed. |
logFile | The path to a file to be used for logging ArchR output. |