runKNN: Run SnapATAC KNN.
In beyondpie/pureRUtils: Commonly used R functions with pure R codes

runKNN

R Documentation

Run SnapATAC KNN.

Description

It will check snapLandmark and snapQuery firstly, if snapLandmark is not NULL, will use it. if snapQuery then is also NULL, will merge them. if both of them are NULL, then use snapAllFile, snapAll in order.

Usage

runKNN(
  snapAll = NULL,
  snapAllFile = NULL,
  snapLandmark = NULL,
  snapLandmarkFile = NULL,
  snapQuery = NULL,
  snapQueryFile = NULL,
  removeBmat = TRUE,
  removeJmat = TRUE,
  k = 50,
  dims = 1:30,
  method = "RANN",
  runUMAP = TRUE,
  umapNcores = 1,
  outmmtxFile = NULL,
  outSnapFile = NULL
)

Arguments

`snapAll`	SnapObject, default NULL
`snapAllFile`	characters, default NULL
`snapLandmark`	SnapObject, default NULL
`snapLandmarkFile`	characters, default NULL
`snapQuery`	SnapObject, default NULL
`snapQueryFile`	SnapObject, default NULL
`removeBmat`	bool, default TRUE
`removeJmat`	bool, default TRUE
`k`	integer, default 50
`dims`	integer or vector, default is 1:30
`method`	characters, method for KNN (either "RANN" or "Annoy") default "RANN"
`runUMAP`	bool, default TRUE
`umapNcores`	integer, default 1
`outmmtxFile`	characters, output file of mmtx, default NULL
`outSnapFile`	characters, default NULL