finemapAim: Wrapper for fine-mapping method described in...

In liangyy/finemapAim: Wrapper for AIM

Description

Please refer to https://github.com/jzou1115/aim and the manuscript for the details of the general workflow.

Usage

finemapAim(
  eqtl,
  geno1,
  geno2,
  y1,
  y2,
  ase_internal = TRUE,
  path_to_aim = NULL,
  temp_dir = ".",
  temp_prefix = "temp"
)

Arguments

eqtl	A vector describing eQTL summary statistic data. It should be z-score.
geno1	A matrix containing genotype data of haplotype 1 (individual x SNP). The SNP order should be the same as eqtl.
geno2	A matrix containing genotype data of haplotype 1 (individual x SNP). The SNP order should be the same as eqtl and the individual order should be the same as geno1.
y1	A vector describing the allele-specific count data of haplotype 1. The individual order should be the same as geno1.
y2	A vector describing the allele-specific count data of haplotype 2. The individual order should be the same as geno1.
ase_internal	A logical scalar telling whether to use internal function for ASE calculation.
path_to_aim	This function relies on external Java executable at https://github.com/jzou1115/aim/blob/master/aim.jar so here please provide the path to the JAR file.
temp_dir	Directory for temporary files.
temp_prefix	Prefix of the temporary files.

Details

The preparation of AIM summary statistics and the corresponding correlation matrices follow the original method. But here we apply susieR::susie_rss for the actual fine-mapping call instead of CAVIAR (which was used in the original paper). This change is simply to speed up the computation when we want to work on thousands of SNPs within a regulatory window. Among the two meta-analysis scheme (S^M1 and S^M2), we report the fine-mapping result of the one with smaller 95

Value

a list containing PIP and 95

Examples

## Not run: 
nsnp = 100
nindiv = 200
eqtl = rnorm(nsnp)
eqtl[1] = 12.5
eqtl[10] = 8.3
geno1 = matrix(sample(c(0, 1), nindiv * nsnp, replace = T), ncol = nsnp)
geno2 = matrix(sample(c(0, 1), nindiv * nsnp, replace = T), ncol = nsnp)
y1 = geno1[, 1] * 8 + geno1[, 10] * 5 + rpois(nindiv, 5)
y2 = geno2[, 1] * 8 + geno2[, 10] * 5 + rpois(nindiv, 5)
e = finemapAim(
  eqtl, geno1, geno2, y1, y2,
  path_to_aim = 'path_to_aim_repo/aim.jar',
  temp_dir = '.',
  temp_prefix = 'test_finemapAim')

## End(Not run)

liangyy/finemapAim documentation built on Sept. 4, 2020, 9:51 p.m.