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:Junwei Han [aut, cre, cph], Yalan He [aut], Xiangmei Li [aut]

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

Datasets:

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

On CRAN:

13 exports 0.63 score 175 dependencies 2 scripts 194 downloads

Last updated 2 years agofrom:b638d23176. Checks:OK: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 03 2024

Exports:get_Entrez_ID get_final_signature get_km_survival_curve get_MultivariateCox_result get_mut_status get_Oncoplots get_pfs_score get_response_plot get_risk_score get_roc_curve get_sam_cla get_univarCox_result newspia

Dependencies:abind AnnotationDbi ape aplot askpass backports BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob boot broom cachem car carData cli clusterProfiler codetools colorspace commonmark corrplot cowplot cpp11 crayon curl data.table DBI Deriv digest DNAcopy doBy DOSE dplyr enrichplot evaluate exactRankTests fansi farver fastmap fastmatch fgsea foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData ggforce ggfun ggnewscale ggplot2 ggplotify ggpubr ggraph ggrepel ggsci ggsignif ggtext ggtree glmnet glue GO.db GOSemSim graphlayouts gridExtra gridGraphics gridtext gson gtable highr httr igraph IRanges isoband iterators jpeg jsonlite KEGGREST km.ci KMsurv knitr labeling lambda.r lattice lazyeval lifecycle lme4 maftools magrittr markdown MASS Matrix MatrixModels maxstat memoise mgcv microbenchmark mime minqa modelr munsell mvtnorm nlme nloptr nnet numDeriv openssl org.Hs.eg.db patchwork pbkrtest pillar pkgconfig plogr plyr png polyclip polynom pROC purrr quantreg qvalue R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 Rhtslib rlang RSQLite rstatix S4Vectors scales scatterpie shadowtext shape snow SparseM stringi stringr survival survminer survMisc sys systemfonts tibble tidygraph tidyr tidyselect tidytree treeio tweenr UCSC.utils utf8 vctrs viridis viridisLite withr xfun xml2 xtable XVector yaml yulab.utils zlibbioc zoo

PMAPscore

Junwei Han,Yalan He,Xiangmei Li

Rendered fromPMAPscore.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2022-05-31
Started: 2022-05-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
final_signature, the final prognosis-related pathways	final_signature
gene_symbol_Entrez, the genes' symbol and ENTREZID	gene_symbol_Entrez
gene_Ucox	gene_Ucox
gene_Ucox_res, the univariate Cox regression result of candidate genes.	gene_Ucox_res
Convert gene symbol to Entrez_Gene_ID	get_Entrez_ID
Identify the candidate prognosis-related pathways	get_final_signature
Plot Kaplan-Meier survival curve.	get_km_survival_curve
Perform the multivariate Cox regression	get_MultivariateCox_result
Converts MAF file into mutation matrix	get_mut_status
draw an GenePathwayOncoplots	get_Oncoplots
Calculates the pathway-based mutation accumulate perturbation score	get_pfs_score
Plot the response column diagram	get_response_plot
Calculates the risk score for patients	get_risk_score
Plot the ROC curve	get_roc_curve
get_sam_cla	get_sam_cla
Perform the univariate Cox regression analysis.	get_univarCox_result
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
newspia	newspia
path_cox_data	path_cox_data
path_gene	path_gene
path_Ucox_mul	path_Ucox_mul
path_Ucox_mul_res	path_Ucox_mul_res
pfs_score	pfs_score
response	response
roc_data, the data frame use for ploting ROC curve	roc_data
sig	sig
sur	sur
symbol_Entrez	symbol_Entrez