Function to perform TWAS analysis for across multiple contexts. This function peforms TWAS analysis for multiple contexts for imputable genes within an LD region and summarize the twas results.

Function to perform TWAS analysis for across multiple contexts. This function peforms TWAS analysis for multiple contexts for imputable genes within an LD region and summarize the twas results.

Usage

twas_pipeline(
  twas_weights_data,
  ld_meta_file_path,
  gwas_meta_file,
  region_block,
  rsq_cutoff = 0.01,
  rsq_pval_cutoff = 0.05,
  rsq_option = c("rsq", "adj_rsq"),
  rsq_pval_option = c("pval", "adj_rsq_pval"),
  mr_pval_cutoff = 0.05,
  mr_coverage_column = "cs_coverage_0.95",
  quantile_twas = FALSE,
  output_twas_data = FALSE,
  event_filters = NULL,
  column_file_path = NULL,
  comment_string = "#"
)

Arguments

twas_weights_data

List of list of twas weights output from generate_twas_db function.

region_block

A string with LD region informaiton of chromosome number, star and end position of LD block conneced with "_".

Value

A list of list containing twas result table and formatted TWAS data compatible with ctwas_sumstats() function.

• twas_table A dataframe of twas results summary is generated for each gene-contexts-method pair of all methods for imputable genes.

• twas_data A list of list containing formatted TWAS data.