run_tests: run_tests.R

In ryanrsun/LungCancerAssoc: Pathway Analysis Using Summary Statistics

Description

Run GHC, GBJ, and minP on the summmary statistics.

Usage

run_tests(snp_mat, combined_Gmat_record, P_mat = P_mat, run_GHC = FALSE,
  checkpoint = TRUE)

Arguments

snp_mat	This is the n*p matrix of genotypes from your reference panel. Hopefully the temp_Gmat variable from prune_snps().
combined_Gmat_record	The snp information data frame, hopefully the one output from prune_snps().
P_mat	Projection matrix for estimation of covariance matrix.
run_GHC	Boolean, if true run both GBJ and GHC, otherwise just GBJ.
checkpoint	Boolean, true if you would like to print diagnostic information.

Value

A list with the elements GBJ, GBJ_p, GBJ_err, GHC, GHC_p, GHC_err, and num_large_Z (number of test statistics greater than 8.2 in magnitude, which R cannot deal with well).

ryanrsun/LungCancerAssoc documentation built on May 24, 2019, 7:26 p.m.