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

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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.

Author
Nathan Lawlor [aut, cre], Peiyong Guan [aut], Alec Fabbri [aut], Krish Karuturi [aut], Joshy George [aut]
Date of publication
None
Maintainer
Nathan Lawlor <nathan.lawlor03@gmail.com>
License
GPL (>= 2)
Version
1.4.0

View on Bioconductor

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.

Files in this package

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