This function processes GWAS and xQTL finemapped data files and then computes QTL enrichment. For details on the parameters `pi_gwas`, `pi_qtl`, `lambda`, `ImpN`, and `num_threads`, refer to the documentation of the `compute_qtl_enrichment` function.
Usage
xqtl_enrichment_wrapper(
xqtl_files,
gwas_files,
xqtl_finemapping_obj = NULL,
gwas_finemapping_obj = NULL,
xqtl_varname_obj = NULL,
gwas_varname_obj = NULL,
num_gwas = NULL,
pi_qtl = NULL,
lambda = 1,
ImpN = 25,
double_shrinkage = FALSE,
bessel_correction = TRUE,
num_threads = 1
)Arguments
- xqtl_files
Vector of xQTL RDS file paths.
- gwas_files
Vector of GWAS RDS file paths.
- xqtl_finemapping_obj
Optional table name in xQTL RDS files (default 'susie_fit').
- gwas_finemapping_obj
Optional table name in GWAS RDS files (default 'susie_fit').
- xqtl_varname_obj
Optional table name in xQTL RDS files (default 'susie_fit').
- gwas_varname_obj
Optional table name in GWAS RDS files (default 'susie_fit').
- pi_qtl
Optional parameter for xQTL enrichment estimation (see `compute_qtl_enrichment`).
- lambda
Shrinkage parameter for enrichment computation (see `compute_qtl_enrichment`).
- ImpN
Importance parameter for enrichment computation (see `compute_qtl_enrichment`).
- num_threads
Number of threads for parallel processing (see `compute_qtl_enrichment`).
- pi_gwas
Optional parameter for GWAS enrichment estimation (see `compute_qtl_enrichment`).
Examples
gwas_files <- c("gwas_file1.rds", "gwas_file2.rds")
xqtl_files <- c("xqtl_file1.rds", "xqtl_file2.rds")
result <- xqtl_enrichment_wrapper(gwas_files, xqtl_files)
#> Warning: cannot open compressed file 'xqtl_file1.rds', probable reason 'No such file or directory'
#> Error in map(gwas_files, function(file) { raw_data <- readRDS(file)[[1]] gwas_data <- if (!is.null(gwas_finemapping_obj)) get_nested_element(raw_data, gwas_finemapping_obj) else raw_data pip <- gwas_data$pip if (!is.null(gwas_varname_obj)) names(pip) <- get_nested_element(raw_data, gwas_varname_obj) pip}): ℹ In index: 1.
#> Caused by error in `gzfile()`:
#> ! cannot open the connection