addGroupCoverages.Rd
This function will merge cells within each designated cell group for the generation of pseudo-bulk replicates and then merge these replicates into a single insertion coverage file.
addGroupCoverages( ArchRProj = NULL, groupBy = "Clusters", useLabels = TRUE, minCells = 40, maxCells = 500, maxFragments = 25 * 10^6, minReplicates = 2, maxReplicates = 5, sampleRatio = 0.8, kmerLength = 6, threads = getArchRThreads(), returnGroups = FALSE, parallelParam = NULL, force = FALSE, verbose = TRUE, logFile = createLogFile("addGroupCoverages") )
ArchRProj | An |
---|---|
groupBy | The name of the column in |
useLabels | A boolean value indicating whether to use sample labels to create sample-aware subgroupings during as pseudo-bulk replicate generation. |
minCells | The minimum number of cells required in a given cell group to permit insertion coverage file generation. |
maxCells | The maximum number of cells to use during insertion coverage file generation. |
maxFragments | The maximum number of fragments per cell group to use in insertion coverage file generation. This prevents the generation of excessively large files which would negatively impact memory requirements. |
minReplicates | The minimum number of pseudo-bulk replicates to be generated. |
maxReplicates | The maximum number of pseudo-bulk replicates to be generated. |
sampleRatio | The fraction of the total cells that can be sampled to generate any given pseudo-bulk replicate. |
kmerLength | The length of the k-mer used for estimating Tn5 bias. |
threads | The number of threads to be used for parallel computing. |
returnGroups | A boolean value that indicates whether to return sample-guided cell-groupings without creating coverages.
This is used mainly in |
parallelParam | A list of parameters to be passed for biocparallel/batchtools parallel computing. |
force | A boolean value that indicates whether or not to overwrite the relevant data in the |
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. |