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RNAseqCovarImpute

Impute Covariate Data in RNA Sequencing Studies


Bioconductor version: Release (3.18)

The RNAseqCovarImpute package implements multiple imputation of missing covariates and differential gene expression analysis by: 1) Randomly binning genes into smaller groups, 2) Creating M imputed datasets separately within each bin, where the imputation predictor matrix includes all covariates and the log counts per million (CPM) for the genes within each bin, 3) Estimating gene expression changes using voom followed by lmFit functions, separately on each M imputed dataset within each gene bin, 4) Un-binning the gene sets and stacking the M sets of model results before applying the squeezeVar function to apply a variance shrinking Bayesian procedure to each M set of model results, 5) Pooling the results with Rubins’ rules to produce combined coefficients, standard errors, and P-values, and 6) Adjusting P-values for multiplicity to account for false discovery rate (FDR).

Author: Brennan Baker [aut, cre] , Sheela Sathyanarayana [aut], Adam Szpiro [aut], James MacDonald [aut], Alison Paquette [aut]

Maintainer: Brennan Baker <brennanhilton at gmail.com>

Citation (from within R, enter citation("RNAseqCovarImpute")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RNAseqCovarImpute")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RNAseqCovarImpute")
Example Data for RNAseqCovarImpute HTML R Script
Impute Covariate Data in RNA-sequencing Studies HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software
Version 1.0.2
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License GPL-3
Depends R (>= 4.3.0)
Imports Biobase, BiocParallel, stats, limma, dplyr, magrittr, rlang, edgeR, foreach, mice
System Requirements
URL https://github.com/brennanhilton/RNAseqCovarImpute
Bug Reports https://github.com/brennanhilton/RNAseqCovarImpute/issues
See More
Suggests BiocStyle, knitr, rmarkdown, tidyr, stringr, testthat (>= 3.0.0)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package RNAseqCovarImpute_1.0.2.tar.gz
Windows Binary RNAseqCovarImpute_1.0.2.zip (64-bit only)
macOS Binary (x86_64) RNAseqCovarImpute_1.0.2.tgz
macOS Binary (arm64) RNAseqCovarImpute_1.0.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/RNAseqCovarImpute
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RNAseqCovarImpute
Bioc Package Browser https://code.bioconductor.org/browse/RNAseqCovarImpute/
Package Short Url https://bioconductor.org/packages/RNAseqCovarImpute/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive