View source: R/GroupCoverages.R
addGroupCoverages | R Documentation |
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,
sampleLabels = "Sample",
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. |
sampleLabels |
The name of a column in |
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. |
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