Package: PMAPscore 0.1.1
PMAPscore: Identify Prognosis-Related Pathways Altered by Somatic Mutation
We innovatively defined a pathway mutation accumulate perturbation score (PMAPscore) to reflect the position and the cumulative effect of the genetic mutations at the pathway level. Based on the PMAPscore of pathways, identified prognosis-related pathways altered by somatic mutation and predict immunotherapy efficacy by constructing a multiple-pathway-based risk model (Tarca, Adi Laurentiu et al (2008) <doi:10.1093/bioinformatics/btn577>).
Authors:
PMAPscore_0.1.1.tar.gz
PMAPscore_0.1.1.tar.gz(r-4.4-noble)
PMAPscore_0.1.1.tgz(r-4.4-emscripten)PMAPscore_0.1.1.tgz(r-4.3-emscripten)
PMAPscore.pdf |PMAPscore.html✨
PMAPscore/json (API)
| # Install 'PMAPscore' in R: |
| install.packages('PMAPscore', repos = c('https://hanjunwei-lab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hanjunwei-lab/pmapscore/issues
- final_signature - Final_signature, the final prognosis-related pathways
- gene_Ucox - Gene_Ucox
- gene_Ucox_res - Gene_Ucox_res, the univariate Cox regression result of candidate genes.
- gene_symbol_Entrez - Gene_symbol_Entrez, the genes' symbol and ENTREZID
- km_data - Km_data
- maf_data - Maf_data
- maffile - Maffile
- mut_num - Mut_num
- mut_sam - Mut_sam
- mut_sample - Mut_sample
- mut_status - Mut_status
- path_Ucox_mul - Path_Ucox_mul
- path_Ucox_mul_res - Path_Ucox_mul_res
- path_cox_data - Path_cox_data
- path_gene - Path_gene
- pfs_score - Pfs_score
- response - Response
- roc_data - Roc_data, the data frame use for ploting ROC curve
- sig - Sig
- sur - Sur
- symbol_Entrez - Symbol_Entrez
Last updated 2 years agofrom:b638d23176. Checks:OK: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 02 2024 |
Exports:get_Entrez_IDget_final_signatureget_km_survival_curveget_MultivariateCox_resultget_mut_statusget_Oncoplotsget_pfs_scoreget_response_plotget_risk_scoreget_roc_curveget_sam_claget_univarCox_resultnewspia
Dependencies:abindAnnotationDbiapeaplotaskpassbackportsBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbootbroomcachemcarcarDatacliclusterProfilercodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncurldata.tableDBIDerivdigestDNAcopydoByDOSEdplyrenrichplotevaluateexactRankTestsfansifarverfastmapfastmatchfgseaforeachformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggpubrggrepelggsciggsignifggtangleggtextggtreeglmnetglueGO.dbGOSemSimgridExtragridGraphicsgridtextgsongtablehighrhttrigraphIRangesisobanditeratorsjpegjsonliteKEGGRESTkm.ciKMsurvknitrlabelinglambda.rlatticelazyevallifecyclelme4maftoolsmagrittrmarkdownMASSMatrixMatrixModelsmaxstatmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellmvtnormnlmenloptrnnetnumDerivopensslorg.Hs.eg.dbpatchworkpbkrtestpheatmappillarpkgconfigplogrplyrpngpolyclippolynompROCpurrrquantregqvalueR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenreshape2RhtslibrlangRSQLiterstatixS4VectorsscalesscatterpieshapesnowSparseMstringistringrsurvivalsurvminersurvMiscsyssystemfontstibbletidyrtidyselecttidytreetreeiotweenrUCSC.utilsutf8vctrsviridisLitewithrxfunxml2xtableXVectoryamlyulab.utilszlibbioczoo
