rqt
This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/rqt.html Contributions: https://github.com/izhbannikov/rqt. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=rqt or https://github.com/izhbannikov/rqt/issues.
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
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○.zenodo.json file
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○DOI references
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○Academic publication links
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○Committers with academic emails
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.3%) to scientific vocabulary
Repository
This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/rqt.html Contributions: https://github.com/izhbannikov/rqt. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=rqt or https://github.com/izhbannikov/rqt/issues.
Basic Info
Statistics
- Stars: 2
- Watchers: 1
- Forks: 2
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
rqt: utilities for gene-level meta-analysis
Installation
Release version
rqt is currently accepted into Bioconductor: https://github.com/Bioconductor/Contributions/issues/212
and hence requires the version of R >=3.4 and the version of Bioconductor of 3.5.
If you have these installed, then rqt can be installed from Github using biocLite:
source("https://bioconductor.org/biocLite.R")
biocLite("rqt")
Developing version
The last version of rqt can be downloaded using devtools:
devtools::install_github("izhbannikov/rqt@devel", buildVignette=TRUE)
Usage
Single dataset
``` library(rqt)
Loading data and constructing the objects
data <- data.matrix(read.table(system.file("extdata/test.bin1.dat", package="rqt"), header=TRUE)) pheno <- data[,1] geno <- data[, 2:dim(data)[2]] colnames(geno) <- paste(seq(1, dim(geno)[2])) geno.obj <- SummarizedExperiment(geno) obj <- rqt(phenotype=pheno, genotype=geno.obj)
Analysis
res <- geneTest(obj, method="pca", out.type = "D") print(res) ```
Multiple datasets (meta analysis)
``` library(rqt) data1 <- data.matrix(read.table(system.file("extdata/phengen2.dat", package="rqt"), skip=1)) pheno <- data1[,1] geno <- data1[, 2:dim(data1)[2]] colnames(geno) <- paste(seq(1, dim(geno)[2])) geno.obj <- SummarizedExperiment(geno) obj1 <- rqt(phenotype=pheno, genotype=geno.obj)
data2 <- data.matrix(read.table(system.file("extdata/phengen3.dat", package="rqt"), skip=1)) pheno <- data2[,1] geno <- data2[, 2:dim(data2)[2]] colnames(geno) <- paste(seq(1, dim(geno)[2])) geno.obj <- SummarizedExperiment(geno) obj2 <- rqt(phenotype=pheno, genotype=geno.obj)
data3 <- data.matrix(read.table(system.file("extdata/phengen.dat", package="rqt"), skip=1)) pheno <- data3[,1] geno <- data3[, 2:dim(data3)[2]] colnames(geno) <- paste(seq(1, dim(geno)[2])) geno.obj <- SummarizedExperiment(geno) obj3 <- rqt(phenotype=pheno, genotype=geno.obj)
res.meta <- geneTestMeta(list(obj1, obj2, obj3)) print(res.meta) ```
Owner
- Name: Ilya Zhbannikov
- Login: izhbannikov
- Kind: user
- Repositories: 25
- Profile: https://github.com/izhbannikov
GitHub Events
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Last Year
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| i.zhbannikov | z****a@g****m | 5 |
| hpages@fhcrc.org | h****s@f****g@b****8 | 3 |
| i.zhbannikov | i****v@b****8 | 3 |
| mtmorgan@fhcrc.org | m****n@f****g@b****8 | 1 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
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Total downloads:
- bioconductor 12,341 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: rqt
rqt: utilities for gene-level meta-analysis
- Homepage: https://github.com/izhbannikov/rqt
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/rqt/inst/doc/rqt.pdf
- License: GPL
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Latest release: 1.34.0
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.4 depends
- SummarizedExperiment * depends
- CompQuadForm * imports
- Matrix * imports
- RUnit * imports
- car * imports
- glmnet * imports
- metap * imports
- methods * imports
- pls * imports
- ropls * imports
- stats * imports
- utils * imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests