addHarmony | R Documentation |
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 |
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 |
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