SamSPECTRAL: Identifies cell population in flow cytometry data.
Version 1.30.0

Samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting "connected components" estimate biological cell populations in the data sample. For instructions on manual installation, refer to the PDF file provided in the following documentation.

Browse man pages Browse package API and functions Browse package files

AuthorHabil Zare and Parisa Shooshtari
Bioconductor views Cancer CellBiology Clustering FlowCytometry HIV StemCells
Date of publicationNone
MaintainerHabil Zare <zare@txstate.edu>
LicenseGPL (>= 2)
Version1.30.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SamSPECTRAL")

Man pages

Building_Communities: Builds the communities from the set of all data points.
check.SamSPECTRAL.input: Checks the input to SamSPECTRAL.
Civilized_Spectral_Clustering: Runs the spectral clustering algorithm on the sample points.
Conductance_Calculation: Computes the conductance between communities.
Connecting: Combines the spectral clusters to build the connected...
eigen.values.10: Eigenvalues for building the SamSPECTRAL vignette.
eigen.values.1000: Eigenvalues for building the SamSPECTRAL vignette.
kneepointDetection: Fits 2 regression lines to data to estimate the knee (or...
SamSPECTRAL: Identifies the cell populations in flow cytometry data.
SamSPECTRAL-package: Identifying cell populations in flow cytometry data.
small: Flow cytometry data to test SamSPECTRAL algorithm.
stmFSC: Flow cytometry data to test SamSPECTRAL algorithm.

Functions

Building_Communities Man page Source code
Civilized_Spectral_Clustering Man page Source code
ClusteringResult Man page
ClusteringResult-class Man page
Conductance_Calculation Man page Source code
Connecting Man page Source code
First.lib Source code
SamSPECTRAL Man page Man page Source code
SamSPECTRAL-package Man page
check.SamSPECTRAL.input Man page Source code
eigen.values.10 Man page
eigen.values.1000 Man page
kneepointDetection Man page Source code
small Man page
stmFSC Man page

Files

DESCRIPTION
NAMESPACE
R
R/Building_Communities.R
R/Civilized_Spectral_Clustering.R
R/Conductance_Calculation.R
R/Connecting.R
R/SamSPECTRAL.R
R/check.SamSPECTRAL.input.R
R/kneepointDetection.R
build
build/vignette.rds
data
data/eigen.values.10.RData
data/eigen.values.1000.RData
data/small_data.RData
data/stm.RData
inst
inst/CITATION
inst/doc
inst/doc/Clustering_by_SamSPECTRAL.R
inst/doc/Clustering_by_SamSPECTRAL.Rnw
inst/doc/Clustering_by_SamSPECTRAL.pdf
man
man/Building_Communities.Rd
man/Civilized_Spectral_Clustering.Rd
man/Conductance_Calculation.Rd
man/Connecting.Rd
man/SamSPECTRAL-package.Rd
man/SamSPECTRAL.Rd
man/check.SamSPECTRAL.input.Rd
man/eigen.values.10.Rd
man/eigen.values.1000.Rd
man/kneepointDetection.Rd
man/small.Rd
man/stmFSC.Rd
src
src/Rinit.c
src/conductance_computation.c
src/maximum_of_rows.c
vignettes
vignettes/Clustering_by_SamSPECTRAL.Rnw
SamSPECTRAL documentation built on May 20, 2017, 11:01 p.m.