SimS: Calculate the initial similarity matrix

In RCSL: Rank Constrained Similarity Learning for Single Cell RNA Sequencing Data

Description

Calculate the initial similarity matrix

Usage

SimS(
  data,
  pcRatio = 0.95,
  gamma = 0.8,
  NN.method = "KNN",
  Dis.method = "Euclidean",
  LSH.TreeNum = 30,
  LSH.Dim = 1000,
  LSH.Dis = "angular",
  neiRatio = 0.65
)

Arguments

data	gene expression matrix after genes filtering
pcRatio	the ratio between the variance of the
gamma	the ratio of the global simialrity
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

initial similarity matrix S

gene expression matrix after PCA processing drData

Examples

gfData <- GenesFilter(yan[1:100,1:15])
res_Sims <- SimS(gfData)
res_Sims$S
res_Sims$res_pca

RCSL documentation built on April 19, 2021, 9:06 a.m.