Package: rqt 1.39.0

Ilya 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:Ilya Zhbannikov [aut, cre], Konstantin Arbeev [aut], Anatoliy Yashin [aut]

rqt_1.39.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rqt/json (API)

# 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-1.39.0(bioc 3.24)rqt-1.38.0(bioc 3.23)

genomewideassociation regression survival principalcomponent statisticalmethod sequencing

4.30 score 2 stars 4 scripts 1 mentions 7 exports 147 dependencies

Last updated from:c2bb3beff9. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	323
linux-devel-x86_64	OK	390
source / vignettes	OK	351
linux-release-x86_64	OK	391
macos-release-arm64	OK	228
macos-oldrel-arm64	OK	169
windows-devel	OK	217
windows-release	OK	202
windows-oldrel	OK	220
wasm-release	OK	214

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 crosstalk curl data.table DelayedArray DEoptimR Deriv digest doBy dplyr evaluate farver fastmap fontawesome foreach forecast Formula fracdiff fs generics GenomicRanges ggplot2 ggrepel glmnet glue gtable highr htmltools htmlwidgets httr IRanges isoband iterators jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle limma lme4 lmtest magrittr MASS mathjaxr Matrix MatrixGenerics MatrixModels matrixStats memoise metap mgcv mime minqa mnormt modelr multcomp MultiAssayExperiment MultiDataSet multtest mutoss mvtnorm nlme nloptr nnet numDeriv openssl otel pbkrtest pillar pkgconfig plotly plotrix pls promises purrr qqconf qqman quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang rmarkdown robustbase ropls RUnit S4Arrays S4Vectors S7 sandwich sass scales Seqinfo shape sn SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys TFisher TH.data tibble tidyr tidyselect timeDate tinytex urca utf8 vctrs viridisLite withr xfun XVector yaml zoo

Using RQT, an R package for gene-level meta-analysis

Overview | Methods in brief | Installation of \emph{rqt} package | Data description | Single dataset | Meta-analysis | Examples | Gene-level analysis on a single dataset | Dichotomous phenotype | Continuous phenotype | Preprocessing with Partial Least Square regression (PLS) | Preprocessing with Partial Least Square Discriminant Analysis (PLS-DA) | Using additional covariates | Session information

Rendered fromrqt-vignette.Rmdusingknitr::rmarkdown

Last update: 2024-08-01
Started: 2017-03-01

Citation

Development and contributors

Readme and manuals

Help Manual

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
get.reg.family	geneTestOne
This function performs an access to genotype.	genotype genotype,rqt-method
Get a given STT	get.a
get.reg.family	get.reg.family
This function performs an access to phenotype	phenotype phenotype,rqt-method
Preprocess input data with Principal Component Analysis method (PCA)	preprocess
preprocessLASSO	preprocessLASSO
preprocessPCA	preprocessPCA
preprocessPLS	preprocessPLS
preprocessLASSO	preprocessRidge
This function performs an access to covariates	results results,rqt-method
Importing required packages and functions	ridge_se
The rqt class constructor	rqt
The rqt class	rqt-class
General functions of 'rqt' such as accessors and printing.	print.rqt rqt-general show.rqt summary.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