Package: rqt 1.31.0

Ilya Y. Zhbannikov

rqt: rqt: utilities for gene-level meta-analysis

Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: "Gene-set association tests for next-generation sequencing data" by Lee et al (2016), Bioinformatics, 32(17), i611-i619, <doi:10.1093/bioinformatics/btw429>.

Authors:I. Y. Zhbannikov, K. G. Arbeev, A. I. Yashin.

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# Install 'rqt' in R:

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

Bug tracker:https://github.com/izhbannikov/rqt/issues

On BioConductor:rqt-1.31.0(bioc 3.20)rqt-1.30.0(bioc 3.19)

bioconductor-package

7 exports 1.00 score 144 dependencies 1 mentions

Last updated 2 months agofrom:5002bfa5c2

Exports:covariates geneTest geneTestMeta genotype phenotype results rqt

Dependencies:abind askpass backports base64enc Biobase BiocBaseUtils BiocGenerics boot broom bslib cachem calibrate car carData cli codetools colorspace CompQuadForm cowplot cpp11 crayon crosstalk curl data.table DelayedArray DEoptimR Deriv digest doBy dplyr evaluate fansi farver fastmap fontawesome foreach fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggrepel glmnet glue gtable highr htmltools htmlwidgets httr IRanges isoband iterators jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle limma lme4 magrittr MASS mathjaxr Matrix MatrixGenerics MatrixModels matrixStats memoise metap mgcv microbenchmark mime minqa mnormt modelr multcomp MultiAssayExperiment MultiDataSet multtest munsell mutoss mvtnorm nlme nloptr nnet numDeriv openssl pbkrtest pillar pkgconfig plotly plotrix pls promises purrr qqconf qqman quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppEigen Rdpack rlang rmarkdown robustbase ropls RUnit S4Arrays S4Vectors sandwich sass scales shape sn SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys TFisher TH.data tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml zlibbioc zoo

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
Applies linear of logistic regregression to the data.	build.null.model
This function performs an access to covariates	covariates covariates,rqt-method
This function performs a gene-level test based on combined effect sizes.	geneTest geneTest,rqt-method
This function performs a gene-level meta-analysis based on combined effect sizes.	geneTestMeta geneTestMeta,list-method
This function performs an access to genotype.	genotype genotype,rqt-method
Get a given STT	get.a
This function performs an access to phenotype	phenotype phenotype,rqt-method
Preprocess input data with Principal Component Analysis method (PCA)	preprocess
This function performs an access to covariates	results results,rqt-method
The rqt class constructor	rqt
The rqt class	rqt-class
General functions of 'rqt' such as accessors and printing.	rqt-general show.rqt
Applies linear of logistic regregression to the data.	simple.multvar.reg
vcov_ridge: returns variance-covariance matrix and standard deviation for ridge/LASSO regression object	vcov_ridge

Package: rqt 1.31.0

rqt: rqt: utilities for gene-level meta-analysis

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