multiClust: multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
Version 1.6.0

Clustering is carried out to identify patterns in transcriptomics profiles to determine clinically relevant subgroups of patients. Feature (gene) selection is a critical and an integral part of the process. Currently, there are many feature selection and clustering methods to identify the relevant genes and perform clustering of samples. However, choosing an appropriate methodology is difficult. In addition, extensive feature selection methods have not been supported by the available packages. Hence, we developed an integrative R-package called multiClust that allows researchers to experiment with the choice of combination of methods for gene selection and clustering with ease. Using multiClust, we identified the best performing clustering methodology in the context of clinical outcome. Our observations demonstrate that simple methods such as variance-based ranking perform well on the majority of data sets, provided that the appropriate number of genes is selected. However, different gene ranking and selection methods remain relevant as no methodology works for all studies.

Browse man pages Browse package API and functions Browse package files

AuthorNathan Lawlor [aut, cre], Peiyong Guan [aut], Alec Fabbri [aut], Krish Karuturi [aut], Joshy George [aut]
Bioconductor views Clustering FeatureExtraction GeneExpression Survival
Date of publicationNone
MaintainerNathan Lawlor <nathan.lawlor03@gmail.com>
LicenseGPL (>= 2)
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("multiClust")

Man pages

avg_probe_exp: Function to produce a matrix containing the average...
cluster_analysis: Function to perform Kmeans or Hierarchical clustering...
input_file: Function to read-in the gene expression file and assign gene...
nor.min.max: Function to normalize data to bring values into alignment....
number_clusters: Function to determine the number of clusters to be used to...
number_probes: Function to determine the number of gene probes to select for...
probe_ranking: Function to select for genes using one of the available gene...
surv_analysis: Function to produce Kaplan-Meier Survival Plots of selected...
WriteMatrixToFile: Function to write a data matrix to a text file.

Functions

WriteMatrixToFile Man page Source code
avg_probe_exp Man page Source code
cluster_analysis Man page Source code
input_file Man page Source code
nor.min.max Man page Source code
number_clusters Man page Source code
number_probes Man page Source code
probe_ranking Man page Source code
surv_analysis Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/WriteMatrixToFile.R
R/avg_probe_exp.R
R/cluster_analysis.R
R/input_file.R
R/nor.min.max.R
R/number_clusters.R
R/number_probes.R
R/probe_ranking.R
R/surv_analysis.R
build
build/vignette.rds
inst
inst/doc
inst/doc/multiClust.R
inst/doc/multiClust.Rmd
inst/doc/multiClust.html
inst/extdata
inst/extdata/GSE2034-RFS-clinical-outcome.txt
inst/extdata/GSE2034.normalized.expression.txt
inst/extdata/GSE2034_Breast.SD_Rank.ward.D2.Fixed_Probe_Num.Fixed_Clust_Num.png
inst/unitTests
inst/unitTests/test_WriteMatrixToFile.R
inst/unitTests/test_avg_probe_exp.R
inst/unitTests/test_cluster_analysis.R
inst/unitTests/test_input_file.R
inst/unitTests/test_nor.min.max.R
inst/unitTests/test_number_clusters.R
inst/unitTests/test_number_probes.R
inst/unitTests/test_probe_ranking.R
inst/unitTests/test_surv_analysis.R
man
man/WriteMatrixToFile.Rd
man/avg_probe_exp.Rd
man/cluster_analysis.Rd
man/input_file.Rd
man/nor.min.max.Rd
man/number_clusters.Rd
man/number_probes.Rd
man/probe_ranking.Rd
man/surv_analysis.Rd
tests
tests/runTests.R
vignettes
vignettes/multiClust.Rmd
multiClust documentation built on May 20, 2017, 10:31 p.m.