IntegrateEmbeddings: Integrate low dimensional embeddings
In ibseq/scs-analysis: Tools for Single Cell Genomics

Description Usage Arguments Details Value

Perform dataset integration using a pre-computed Anchorset of specified low dimensional representations.

IntegrateEmbeddings(anchorset, ...)

## S3 method for class 'IntegrationAnchorSet'
IntegrateEmbeddings(
  anchorset,
  new.reduction.name = "integrated_dr",
  reductions = NULL,
  dims.to.integrate = NULL,
  k.weight = 100,
  weight.reduction = NULL,
  sd.weight = 1,
  sample.tree = NULL,
  preserve.order = FALSE,
  verbose = TRUE,
  ...
)

## S3 method for class 'TransferAnchorSet'
IntegrateEmbeddings(
  anchorset,
  reference,
  query,
  new.reduction.name = "integrated_dr",
  reductions = "pcaproject",
  dims.to.integrate = NULL,
  k.weight = 100,
  weight.reduction = NULL,
  reuse.weights.matrix = TRUE,
  sd.weight = 1,
  preserve.order = FALSE,
  verbose = TRUE,
  ...
)

`anchorset`	An AnchorSet object
`...`	Reserved for internal use
`new.reduction.name`	Name for new integrated dimensional reduction.
`reductions`	Name of reductions to be integrated. For a TransferAnchorSet, this should be the name of a reduction present in the anchorset object (for example, "pcaproject"). For an IntegrationAnchorSet, this should be a `DimReduc` object containing all cells present in the anchorset object.
`dims.to.integrate`	Number of dimensions to return integrated values for
`k.weight`	Number of neighbors to consider when weighting anchors
`weight.reduction`	Dimension reduction to use when calculating anchor weights. This can be one of: A string, specifying the name of a dimension reduction present in all objects to be integrated A vector of strings, specifying the name of a dimension reduction to use for each object to be integrated A vector of `DimReduc` objects, specifying the object to use for each object in the integration NULL, in which case the full corrected space is used for computing anchor weights.
`sd.weight`	Controls the bandwidth of the Gaussian kernel for weighting
`sample.tree`	Specify the order of integration. If NULL, will compute automatically.
`preserve.order`	Do not reorder objects based on size for each pairwise integration.
`verbose`	Print progress bars and output
`reference`	Reference object used in anchorset construction
`query`	Query object used in anchorset construction
`reuse.weights.matrix`	Can be used in conjunction with the store.weights parameter in TransferData to reuse a precomputed weights matrix.

The main steps of this procedure are identical to IntegrateData with one key distinction. When computing the weights matrix, the distance calculations are performed in the full space of integrated embeddings when integrating more than two datasets, as opposed to a reduced PCA space which is the default behavior in IntegrateData.

When called on a TransferAnchorSet (from FindTransferAnchors), this will return the query object with the integrated embeddings stored in a new reduction. When called on an IntegrationAnchorSet (from IntegrateData), this will return a merged object with the integrated reduction stored.

ibseq/scs-analysis documentation built on Feb. 27, 2021, 12:35 a.m.