NeigRepresent: Calculate the neighbor representation of cells to the...

In QinglinMei/RCSL: Rank Constrained Similarity Learning for single cell RNA sequencing data

Calculate the neighbor representation of cells to the low-dimensional gene expression matrix

Description

Calculate the neighbor representation of cells to the low-dimensional gene expression matrix

Usage

NeigRepresent(
  drData,
  NN.method = "KNN",
  Dis.method = "Euclidean",
  LSH.TreeNum = 30,
  LSH.Dim = 500,
  LSH.Dis = "angular",
  neiRatio = 0.65
)

Arguments

drData	gene expression matrix after dimensionality reduced by PCA
NN.method	the method of finding neighbors
Dis.method	the distance metric in finding neighbors
LSH.TreeNum	the tree number of LSH
LSH.Dim	the dimension in LSH
LSH.Dis	the distance metric in LSH
neiRatio	ratio of the number of selected

Value

the similarity matrix measured by neighbor representation NR

Examples

gfData <- GenesFilter(yan)
res_SimS <- SimS(gfData)
NeigRepresent(res_SimS$drData)

QinglinMei/RCSL documentation built on Feb. 16, 2024, 2:31 a.m.