RVFam specifications

Information


Unique identifier OMICS_10384
Name RVFam
Alternative name Rare Variant association analysis with Family data
Software type Package/Module
Interface Command line interface
Restrictions to use None
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.
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.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Ming-Huei Chen <>

Publication for Rare Variant association analysis with Family data

RVFam institution(s)
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
RVFam funding source(s)
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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