Package: GSSTDA 1.0.0

GSSTDA: Progression Analysis of Disease with Survival using Topological Data Analysis

Mapper-based survival analysis with transcriptomics data is designed to carry out. Mapper-based survival analysis is a modification of Progression Analysis of Disease (PAD) where survival data is taken into account in the filtering function. More details in: J. Fores-Martos, B. Suay-Garcia, R. Bosch-Romeu, M.C. Sanfeliu-Alonso, A. Falco, J. Climent, "Progression Analysis of Disease with Survival (PAD-S) by SurvMap identifies different prognostic subgroups of breast cancer in a large combined set of transcriptomics and methylation studies" <doi:10.1101/2022.09.08.507080>.

Authors:Miriam Esteve [aut, cre], Raquel Bosch [aut], Jaume Forés [aut], Joan Climent [aut], Antonio Falco [aut]

GSSTDA_1.0.0.tar.gz
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GSSTDA.pdf |GSSTDA.html✨
GSSTDA/json (API)

# Install 'GSSTDA' in R:
install.packages('GSSTDA', repos = c('https://miriamesteve.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/miriamesteve/gsstda/issues

Datasets:

On CRAN:

5.20 score 2 stars 7 scripts 462 downloads 15 exports 118 dependencies

Last updated 4 months agofrom:fddde620fd. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:denoise_rectangular_matrixdsgaflatten_normal_tissgene_selectiongene_selection_generate_disease_componentgsstdalp_norm_k_powers_survmapperone_D_Mapperoptimal_SVHT_coef_gamma_knownoptimal_SVHT_coef_gamma_unknownplot_dsgaplot_mapperresults_dsga

Dependencies:askpassbase64encBiocGenericsbrewbriobslibcachemcallrcirclizeclicliprclueclustercodetoolscolorspacecommonmarkComplexHeatmapcpp11crayoncredentialscurldescdevtoolsdiffobjdigestdoParalleldownlitellipsisevaluatefansifastmapfontawesomeforeachfsgertGetoptLongghgitcredsGlobalOptionsgluehighrhtmltoolshtmlwidgetshttpuvhttr2iniIRangesiteratorsjquerylibjsonliteknitrlaterlatticelifecyclemagrittrMatrixmatrixStatsmemoisemimeminiUIopensslpillarpkgbuildpkgconfigpkgdownpkgloadpngpraiseprettyunitsprocessxprofvispromisespspurrrR6raggrappdirsrcmdcheckRColorBrewerRcpprematch2remotesrjsonrlangrmarkdownroxygen2rprojrootrstudioapirversionsS4Vectorssasssessioninfoshapeshinysourcetoolsstringistringrsurvivalsyssystemfontstestthattextshapingtibbletinytexurlcheckerusethisutf8vctrsvisNetworkwaldowhiskerwithrxfunxml2xopenxtableyamlzip

GSSTDA Vignette: Gene Structure Survival using Topological Data Analysis

Rendered fromGSSTDA-vignette.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-06-01
Started: 2023-04-24

Readme and manuals

Help Manual

Help pageTopics
Case-control vectorcase_tag
check_arg_mappercheck_arg_mapper
check_filter_valuescheck_filter_values
check_full_datacheck_full_data
check_gene_selectioncheck_gene_selection
check_vectorscheck_vectors
Get clusters for all data levelclust_all_levels
Get clusters for a particular data levelclust_lev
Computes the adjacency matrix.compute_node_adjacency
Survival analysis based on gene expression levels.cox_all_genes
Rectangular Matrix Denoiser.denoise_rectangular_matrix
Disease-Specific Genomic Analysisdsga
Flatten normal tissuesflatten_normal_tiss
Gene expression matrixfull_data
Gene selection and filter functiongene_selection
Private gene_selection_gene_selection_
Gene selection based on variability and the relationship to survival.gene_selection_surv
gene_selection_classes.defaultgene_selection.default
gene_selection_classes.dsga_objectgene_selection.dsga_object
Generate disease component matrix.generate_disease_component
Extract intervals from filter function output values.get_intervals_One_D
Gene Structure Survival using Topological Data Analysis (GSSTDA).gsstda
Incomplete Marcenko-Pastur IntegralincMarPas
Extract Information about Nodeslevels_to_nodes
Filtering functionlp_norm_k_powers_surv
Map to colormap_to_color
Mapper objectmapper
Median of the Marcenko-Pastur DistributionMedianMarcenkoPastur
one_D_Mapperone_D_Mapper
Optimal SVHT Coefficient with Known Noise Leveloptimal_SVHT_coef_gamma_known
Optimal SVHT Coefficient with Unknown Noise Leveloptimal_SVHT_coef_gamma_unknown
plot dsgaplot_dsga
Plot mapperplot_mapper
results dsgaresults_dsga
Samples in levelssamples_in_levels
Survival event vectorsurvival_event
Survival time vectorsurvival_time