NEWS0.md

In baolinwu/mkatr: Miscellaneous variant-set association test methods

mkatr

• An R package implementing various statistical methods for testing variant-set association

On sequence-kernel association test of rare variant set

• References
  • Wu,B., Pankow,J.S., Guan,W. (2015) Sequence kernel association analysis of rare variant set based on the marginal regression model for binary traits. Genetic Epidemiology, 39(6), 399-405.
  • Wu,B., Guan,W., Pankow,J.S. (2016) On efficient and accurate calculation of significance p-values for sequence kernel association test of variant set. Annals of human genetics, 80(2), 123-135.
• Sample R codes

library(mkatr)
### simulate outcomes
X = matrix(rnorm(10000), 5000,2)
D = rbinom(5000,1,0.5)
G = matrix(rbinom(100000,2,0.01), 5000,10)
### SKATL and SKATOL tests
SKATL(KAT.null(D,X), G, c(1.5,25.5))
SKATOL(KAT.null(D,X), G, c(1.5,25.5))
### compared to SKAT package
## library(SKAT)
## SKAT(G, SKAT_Null_Model(D ~ X, out_type="D"))$p.value
## SKAT(G, SKAT_Null_Model(D ~ X, out_type="D"), method="optimal.adj")$p.value

SNP-set association tests using GWAS summary data

• Reference
  • Guo,B. and Wu,B. (2018) Statistical methods to detect novel genetic variants using publicly available GWAS summary data. CBC, to appear.
• Implemented in the "sats()" R function returning three test p-values: adaptive test (AT), squared sum test (S2T), sum test (ST)
• Sample R codes r library(mkatr) R = cor(matrix(rnorm(500),100,5)*sqrt(0.8)+rnorm(100)*sqrt(0.2)) Z0 = rnorm(5) sats(Z0,R) Z = Z0 + c(2,3,-1,2,-3) sats(Z,R) Z = Z0 + c(2,3,4,2,3) sats(Z,R)

baolinwu/mkatr documentation built on May 14, 2019, 6:03 a.m.