getFootprints.Rd
This function will get footprints for all samples in a given ArchRProject and return a summarized experiment object that can be used for downstream analyses
getFootprints( ArchRProj = NULL, positions = NULL, plotName = "Plot-Footprints", groupBy = "Clusters", useGroups = NULL, flank = 250, minCells = 25, nTop = NULL, threads = getArchRThreads(), verbose = TRUE, logFile = createLogFile("getFootprints") )
ArchRProj | An |
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positions | A |
plotName | The prefix to add to the file name for the output PDF file containing the footprint plots. |
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 |
flank | The number of basepairs from the position center (+/-) to consider as the flank. |
minCells | The minimum number of cells required in a given cell group to permit footprint generation. |
nTop | The number of genomic regions to consider. Only the top |
threads | The number of threads to be used for parallel computing. |
verbose | A boolean value that determines whether standard output includes verbose sections. |
logFile | The path to a file to be used for logging ArchR output. |