addHarmony.Rd
This function will add the Harmony batch-corrected reduced dimensions to an ArchRProject.
addHarmony( ArchRProj = NULL, reducedDims = "IterativeLSI", dimsToUse = NULL, scaleDims = NULL, corCutOff = 0.75, name = "Harmony", groupBy = "Sample", verbose = TRUE, force = FALSE, ... )
ArchRProj | An |
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reducedDims | The name of the |
dimsToUse | A vector containing the dimensions from the |
scaleDims | A boolean that indicates whether to z-score the reduced dimensions for each cell. This is useful forminimizing the contribution
of strong biases (dominating early PCs) and lowly abundant populations. However, this may lead to stronger sample-specific biases since
it is over-weighting latent PCs. If set to |
corCutOff | A numeric cutoff for the correlation of each dimension to the sequencing depth. If the dimension has a correlation
to sequencing depth that is greater than the |
name | The name to store harmony output as a |
groupBy | The name of the column in |
verbose | A boolean value indicating whether to use verbose output during execution of this function. Can be set to FALSE for a cleaner output. |
force | A boolean value that indicates whether or not to overwrite data in a given column when the value passed to |
... | Additional arguments to be provided to harmony::HarmonyMatrix |