Merge multiple SMR files and keep only shared probes for 2 outcomes

This function finds intersected probeID across all provided files and merges them into a single data frame using inner_join.

Usage

leo_smr_merge_shared_probes(
  dir = NULL,
  file_paths = NULL,
  pattern = "\\.sig\\.all$",
  out_file = ""
)

Arguments

dir

Character. A directory containing SMR files (e.g. ".sig.all" files). If provided, the function will read all matching files in this directory.

file_paths

Character vector. A set of absolute paths to SMR files. (Priority over dir) If this is non-NULL, dir is ignored.

pattern

Character. Regex pattern for searching files in dir. Default is "\.sig\.all$".

out_file

Character. If not empty, write the merged result to this path. Otherwise only return in R.

Value

A tibble containing shared probes across all specified files. If out_file is provided, the result is written to disk and the function returns NULL.

Examples

if (FALSE) { # \dontrun{
# 1) Merge all .sig.all files in a directory:
merged_df <- leo_smr_merge_shared_probes(
  dir = "/path/to/smr-t2d/combine_1outcome/sig"
)

# 2) Merge specific files by absolute paths:
files_vec <- c(
  "/path/to/smr/combine_1outcome/smr_res_20241230_iri3.all",
  "/path/to/smr/combine_1outcome/smr_res_20241230_t1d1.all"
)
merged_df <- leo_smr_merge_shared_probes(
  file_paths = files_vec,
  out_file = "shared_probes_merged.tsv"
)
} # }