Package: pathwayTMB 0.1.3
pathwayTMB: Pathway Based Tumor Mutational Burden
A systematic bioinformatics tool to develop a new pathway-based gene panel for tumor mutational burden (TMB) assessment (pathway-based tumor mutational burden, PTMB), using somatic mutations files in an efficient manner from either The Cancer Genome Atlas sources or any in-house studies as long as the data is in mutation annotation file (MAF) format. Besides, we develop a multiple machine learning method using the sample's PTMB profiles to identify cancer-specific dysfunction pathways, which can be a biomarker of prognostic and predictive for cancer immunotherapy.
Authors:
pathwayTMB_0.1.3.tar.gz
pathwayTMB_0.1.3.zip(r-4.5)pathwayTMB_0.1.3.zip(r-4.4)pathwayTMB_0.1.3.zip(r-4.3)
pathwayTMB_0.1.3.tgz(r-4.4-any)pathwayTMB_0.1.3.tgz(r-4.3-any)
pathwayTMB_0.1.3.tar.gz(r-4.5-noble)pathwayTMB_0.1.3.tar.gz(r-4.4-noble)
pathwayTMB_0.1.3.tgz(r-4.4-emscripten)pathwayTMB_0.1.3.tgz(r-4.3-emscripten)
pathwayTMB.pdf |pathwayTMB.html✨
pathwayTMB/json (API)
| # Install 'pathwayTMB' in R: |
| install.packages('pathwayTMB', repos = c('https://hanjunwei-lab.r-universe.dev', 'https://cloud.r-project.org')) |
- PTMB_matrix - PTMB_matrix, the Pathway-based Tumor Mutational Burden matrix
- final_character - Final_character, the example's final signature
- gene_path - Gene_path, the pathways geneset
- genesmbol - Genesmbol, the coding genes' length
- mut_matrix - Mut_matrix, mutations matrix
- sur - Sur, the samples' survival data
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 years agofrom:848adf6348. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 02 2024 |
| R-4.5-win | NOTE | Sep 02 2024 |
| R-4.5-linux | NOTE | Sep 02 2024 |
| R-4.4-win | NOTE | Sep 02 2024 |
| R-4.4-mac | NOTE | Sep 02 2024 |
| R-4.3-win | NOTE | Sep 02 2024 |
| R-4.3-mac | NOTE | Sep 02 2024 |
Exports:GenePathwayOncoplotsget_final_signatureget_mut_matrixget_PTMBplotKMcurvesplotMutInteractplotROC
Dependencies:abindAnnotationDbiapeaplotaskpassbackportsBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbootbroomcachemcarcarDatacaretclasscliclockclusterProfilercodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncurldata.tableDBIDerivdiagramdigestDNAcopydoByDOSEdplyre1071enrichplotevaluateexactRankTestsfansifarverfastmapfastmatchfgseaforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggpubrggraphggrepelggsciggsignifggtextggtreeglmnetglobalsglueGO.dbGOSemSimgowergraphlayoutsgridExtragridGraphicsgridtextgsongtablehardhathighrhttrigraphipredIRangesisobanditeratorsjpegjsonliteKEGGRESTKernSmoothkm.ciKMsurvknitrlabelinglambda.rlatticelavalazyevallifecyclelistenvlme4lubridatemaftoolsmagrittrmarkdownMASSMatrixMatrixModelsmaxstatmemoisemgcvmicrobenchmarkmimeminqaModelMetricsmodelrmunsellmvtnormnlmenloptrnnetnumDerivopensslparallellypatchworkpbkrtestpillarpkgconfigplogrplyrpngpolyclippolynompROCprodlimprogressrproxypurrrquantregqvalueR.methodsS3R.ooR.utilsR6randomForestRColorBrewerRcppRcppArmadilloRcppEigenrecipesreshape2RhtslibrlangrpartRSQLiterstatixS4VectorsscalesscatterpieshadowtextshapesnowSparseMSQUAREMstringistringrsurvivalsurvminersurvMiscsyssystemfontstibbletidygraphtidyrtidyselecttidytreetimechangetimeDatetreeiotweenrtzdbUCSC.utilsutf8vctrsviridisviridisLitewithrxfunxml2xtableXVectoryamlyulab.utilszlibbioczoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| final_character, the example's final signature | final_character |
| gene_path, the pathways geneset | gene_path |
| draw an GenePathwayOncoplots | GenePathwayOncoplots |
| genesmbol, the coding genes' length | genesmbol |
| Filter cancer-specific dysfunction pathways. | get_final_signature |
| Converts MAF into mutation matrix. | get_mut_matrix |
| Calculate the Pathway-based Tumor Mutational Burden. | get_PTMB |
| mut_matrix, mutations matrix | mut_matrix |
| Drawing Kaplan Meier Survival Curves Using the final survival-related PTMB. | plotKMcurves |
| Exact tests to detect mutually exclusive, co-occuring and altered genesets or pathways. | plotMutInteract |
| plot the ROC curve | plotROC |
| PTMB_matrix, the Pathway-based Tumor Mutational Burden matrix | PTMB_matrix |
| sur, the samples' survival data | sur |
