Package: gwasurvivr 1.31.0

Abbas Rizvi

gwasurvivr: gwasurvivr: an R package for genome wide survival analysis

gwasurvivr is a package to perform survival analysis using Cox proportional hazard models on imputed genetic data.

Authors:Abbas Rizvi, Ezgi Karaesmen, Martin Morgan, Lara Sucheston-Campbell

gwasurvivr_1.31.0.tar.gz
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gwasurvivr_1.31.0.tgz(r-4.6-any)gwasurvivr_1.31.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gwasurvivr/json (API)

# Install 'gwasurvivr' in R:

install.packages('gwasurvivr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/suchestoncampbelllab/gwasurvivr/issues

On BioConductor:gwasurvivr-1.31.0(bioc 3.24)gwasurvivr-1.30.0(bioc 3.23)

genomewideassociation survival regression genetics snp geneticvariability pharmacogenomics biomedicalinformatics

6.54 score 13 stars 88 scripts 426 downloads 1 mentions 5 exports 134 dependencies

Last updated from:be064b4435. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
bioc-checks	ERROR	231
linux-devel-x86_64	OK	622
source / vignettes	OK	402
linux-release-x86_64	OK	585
macos-release-arm64	OK	301
macos-oldrel-arm64	OK	245
windows-devel	OK	447
windows-release	OK	442
windows-oldrel	OK	470
wasm-release	OK	198

Exports:gdsCoxSurv impute2CoxSurv michiganCoxSurv plinkCoxSurv sangerCoxSurv

Dependencies:abind AnnotationDbi askpass backports BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob boot broom BSgenome cachem cigarillo cli clipr codetools cpp11 crayon curl data.table DBI DelayedArray DNAcopy dplyr fastmap forcats foreach formatR formula.tools futile.logger futile.options gdsfmt generics GenomicAlignments GenomicFeatures GenomicRanges glmnet glue GWASExactHW GWASTools haven hms httr IRanges iterators jomo jsonlite KEGGREST lambda.r lattice lifecycle lme4 lmtest logistf magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mice mime minqa mitml nlme nloptr nnet numDeriv openssl operator.tools ordinal pan pillar pkgconfig png prettyunits progress purrr quantreg quantsmooth R6 rbibutils Rcpp RcppEigen RCurl Rdpack readr reformulas restfulr RhpcBLASctl Rhtslib rjson rlang rpart Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sandwich Seqinfo shape snow SNPRelate SparseArray SparseM stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb ucminf utf8 VariantAnnotation vctrs vroom withr XML XVector yaml zoo

gwasurvivr Vignette

Introduction | Main input arguments | Main output format | Getting started | Dependencies | User settings: parallelization setup | R Session Examples | Michigan Imputation Server | Single SNP analysis | SNP with covariate interaction | Sanger Imputation Server | IMPUTE2 Imputation | SNP covariate interaction | plinkCoxSurv | Batch Examples | Batch Example sangerCoxSurv | Batch Example impute2CoxSurv | Batch Example michiganCoxSurv | Session info | References

Rendered fromgwasurvivr_Introduction.Rmdusingknitr::rmarkdown

Last update: 2018-10-04
Started: 2018-05-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Fit Cox survival to all variants from a standard IMPUTE2 output after genotype imputation	gdsCoxSurv
Fit Cox survival to all variants from a standard IMPUTE2 output after genotype imputation	impute2CoxSurv
Fit Cox survival to all variants in a .vcf.gz file from Michigan imputation server	michiganCoxSurv
Fit Cox survival to all variants from PLINK binary files (.BED, .BIM, .FAM)	plinkCoxSurv
Fit Cox survival to all variants in a .vcf.gz file from Sanger imputation server	sangerCoxSurv

Usage by other packages (reverse dependencies)