- Unique identifier:
- Software type:
- Restrictions to use:
- Output data:
- The output from RVFam includes 1) a text file containing single variant test results including beta, se, and p-value, 2) text files of gene based test results, 3) an RData containing score statistics that can be directly used by seqMeta for meta-analyses.
- Programming languages:
- Computer skills:
- Rare Variant association analysis with Family data
- Command line interface
- Input data:
- Input to this package are SNP genotype data coded as 0, 1, and 2 for number of copies of coded allele, phenotype and covariate data, and pedigree data. It also requires gene annotation for each SNP for forming pooled multi-variant tests, a comma delimited file with MAF (based on all genotyped sample), and an RData containing genotype correlation matrix for the defined genes or regions.
- Operating system:
- Unix/Linux, Mac OS, Windows
- GNU General Public License version 2.0
- Documentation: https://cran.r-project.org/web/packages/RVFam/RVFam.pdf
- Ming-Huei Chen <>
No open topic.
(Chen and Yang, 2016)
RVFam: an R package for rare variant association analysis with family data.
PMID: 26508760 DOI: 10.1093/bioinformatics/btv609
Department of Neurology, Boston University School of Medicine, Boston, MA, USA; Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA; Framingham Heart Study, Population Sciences Branch, Division of Intramural Research, National Heart Lung and Blood Institute, National Institutes of Health, Framingham, MA, USA
This work was partially supported by the National Heart, Lung and Blood Institute's Framingham Heart Study (Contract No. N01-HC-25195).
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