gJLS2 (version 0.2.0)

gJLS2s: generalized Joint-Location-Scale (gJLS) test with summary statistics

Description

This function takes as input the gL and gS p-values for each SNP and combine to produce the gJLS p-values. It is used for genome-wide analysis where only the gL or gS p-values are available, caution should be exercised when combing gL and gS p-values obtained from separate datasets.

Usage

gJLS2s(gL, gS)

Arguments

gL

a vector of location p-values or a data.frame containing column names "SNP" and "gL".

gS

a vector of scale p-values or a data.frame containing column names "SNP" and "gS".

Value

a vector of combined gJLS p-values for each SNP.

References

Soave D, Corvol H, Panjwani N, Gong J, Li W, Bo<U+00EB>lle PY, Durie PR, Paterson AD, Rommens JM, Strug LJ, Sun L. (2015). A Joint Location-Scale Test Improves Power to Detect Associated SNPs, Gene Sets, and Pathways. American Journal of Human Genetics. 2015 Jul 2;97(1):125-38. 10.1016/j.ajhg.2015.05.015. PMID: 26140448; PMCID: PMC4572492.

Examples

# NOT RUN {
gL <- data.frame("SNP" = paste("rs", 1:100, sep=""), "gL"=runif(100))
gS <- runif(100)

gJLS2s(gL = gL, gS=gS)


# }