DensVM: Density-based local maxima cluster with SVM

In JinmiaoChenLab/cytofkit2: cytofkit2: an integrated mass cytometry data analysis pipeline. Cytofkit provides functions for data pre-processing, fast clustering, data visualization through linear or non-linear dimensionality reduction, automatic identification of cell subsets, and inference of the relatedness between cell subsets

Density-based local maxima cluster with SVM

Description

Density-based local maxima peak finding, subpopulation assigning with the power of SVM

Usage

DensVM(ydata, xdata)

Arguments

ydata	a matrix of the dimension reduced(transformed) data
xdata	a matrix of the expression data

Value

a list contains a matrix peakdata of the peak numbers with different kernel bandwidth, and a matrix clusters of the cluster results

Author(s)

Chen Jinmiao

Examples

d<-system.file('extdata',package='cytofkit2')
fcsFile <- list.files(d,pattern='.fcs$',full=TRUE)
xdata <- cytof_exprsMerge(fcsFile, mergeMethod = 'fixed', fixedNum = 100)
ydata <- cytof_dimReduction(xdata)
#clusters <- DensVM(ydata, xdata)

JinmiaoChenLab/cytofkit2 documentation built on May 12, 2022, 8:09 a.m.