Run burden test on all transcripts in an isotwas_model

Convenience function to run burdenTest on all transcripts in an isotwas_model or isotwas_result object.

Usage

burdenTest_all(
  model,
  ld,
  gene,
  sumStats,
  chr = NULL,
  pos = NULL,
  a1,
  a2,
  snpName = "SNP",
  Z = NULL,
  beta = NULL,
  se = NULL,
  R2cutoff = 0.01,
  alpha = 2.5e-06,
  nperms = 1000,
  usePos = FALSE,
  verbose = FALSE
)

Arguments

model

An isotwas_model or isotwas_result object

ld

matrix, ld reference matrix with SNP names as row/colnames

gene

character, gene name

sumStats

data frame, GWAS summary statistics

chr

character, colnames in sumStats that keeps the chromosome

pos

character, colnames in sumStats that keeps the position

a1

character, colnames in sumStats that keeps the ALT allele

a2

character, colnames in sumStats that keeps the REF allele

snpName

character, colnames in sumStats that keeps the SNP id

Z

character, colnames in sumStats that keeps the Z score

beta

character, colnames in sumStats that keeps the effect size

se

character, colnames in sumStats that keeps the standard error

R2cutoff

numeric, predictive R2 cutoff

alpha

numeric, P-value threshold for permutation testing

nperms

numeric, number of permutations

usePos

logical, use SNP positions vs. SNP ids

verbose

logical, print progress

Value

data.frame with burden test results for all transcripts