addCombinedDims: Combine two or more modalities dimensionality reductions.
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

addCombinedDims

R Documentation

Combine two or more modalities dimensionality reductions.

Description

This function will combine two or more modalities dimensionality reductions into a single reduction.

Usage

addCombinedDims(
  ArchRProj = NULL,
  name = "CombinedDims",
  reducedDims = NULL,
  dimWeights = NULL,
  dimsToUse = NULL,
  scaleDims = NULL,
  corCutOff = 0.75
)

Arguments

`ArchRProj`	An `ArchRProject` object.
`name`	The name for the combinedDims to be stored as.
`reducedDims`	The name of the `reducedDims` objects (i.e. "IterativeLSI") to use from the designated `ArchRProject`.
`dimWeights`	A vector of weights to be used to weight each dimensionality reduction when combining.
`dimsToUse`	A vector containing the dimensions from the `reducedDims` objects to use.
`scaleDims`	A boolean value that indicates whether to z-score the reduced dimensions for each cell. This is useful for minimizing 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 `NULL` this will scale the dimensions based on the value of `scaleDims` when the `reducedDims` were originally created during dimensionality reduction. This idea was introduced by Timothy Stuart.
`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 `corCutOff`, it will be excluded from analysis.