Robust Variance Score.
The robust variance score (RVS) is a novel likelihood-based method for genetic association with NGS data from external control groups. RVS substitutes genotype calls by their expected values given observed sequence data and implements a robust variance estimate for the score statistic.
Derkach, A et al.
Association Analysis Using Next Generation Sequence Data from Publicly Available Control Groups: The Robust Variance Score Statistic.
Bioinformatics 30 (15): 2179-2188 first published online April 14, 2014. PMID:24733292
- RVS.rar contains the following files, as of Mar 5, 2014:
- Oct 27, 2014: R package core functions release: RVS at github.com.
- Nov 10, 2014: RVS example for NULL case using 1000 snps:
- RVS core R package (same version on github as of Oct 27, 2014): rvs_0.0.tar.gz.
- Example R code for the NULL (no association) case: example_new_NULL.r
- Refer to pg 2182 (section 2.3.1 of publication referenced above)
- Test vcf inputfile containing 1000 snps: 1g113low_1g56exomehigh_filtered.hg19.chr11_1000snps.vcf.
- Test bam inputfile containing IDs for the cases: bam.
- Notes: First download and install RVS and then run example file:
- R --no-save < example_new_NULL.r
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