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Colocalization Analysis Wrapper

Source: R/encoloc.R
coloc_wrapper.Rd

This function processes xQTL and multiple GWAS finemapped data files for colocalization analysis.

Usage

coloc_wrapper(
  xqtl_file,
  gwas_files,
  xqtl_finemapping_obj = NULL,
  xqtl_varname_obj = NULL,
  xqtl_region_obj = NULL,
  gwas_finemapping_obj = NULL,
  gwas_varname_obj = NULL,
  gwas_region_obj = NULL,
  filter_lbf_cs = FALSE,
  filter_lbf_cs_secondary = NULL,
  prior_tol = 1e-09,
  p1 = 1e-04,
  p2 = 1e-04,
  p12 = 5e-06,
  ...
)

Arguments

xqtl_file

Path to the xQTL RDS file.

gwas_files

Vector of paths to GWAS RDS files.

xqtl_finemapping_obj

Optional table name in xQTL RDS files (default 'susie_fit').

xqtl_varname_obj

Optional table name in xQTL RDS files (default 'susie_fit').

xqtl_region_obj

Optional table name in xQTL RDS files (default 'susie_fit').

gwas_finemapping_obj

Optional table name in GWAS RDS files (default 'susie_fit').

gwas_varname_obj

Optional table name in GWAS RDS files (default 'susie_fit').

gwas_region_obj

Optional table name in GWAS RDS files (default 'susie_fit').

prior_tol

When the prior variance is estimated, compare the estimated value to prior_tol at the end of the computation, and exclude a single effect from PIP computation if the estimated prior variance is smaller than this tolerance value.

p1,

p2, and p12 are results from xqtl_enrichment_wrapper (default 'p1=1e-4, p2=1e-4, p12=5e-6', same as coloc.bf_bf).

region_obj

Optional table name of region info in susie_twas output filess (default 'region_info').

Value

A list containing the coloc results and the summarized sets.

Examples

xqtl_file <- "xqtl_file.rds"
gwas_files <- c("gwas_file1.rds", "gwas_file2.rds")
result <- coloc_wrapper(xqtl_file, gwas_files, LD_meta_file_path)
#> Warning: cannot open compressed file 'gwas_file1.rds', probable reason 'No such file or directory'
#> Error in gzfile(file, "rb"): cannot open the connection