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Adjust SMR Results with FDR and Bonferroni Corrections

leo_smr_adjust.Rd

It applies FDR/Bonferroni corrections for a single SMR result. The corrected results are saved in an fdr subdirectory within the output directory.

Usage

leo_smr_adjust(
  smr_result_path,
  writePath = "",
  out_dir = "",
  QTL_type = "",
  Source = "",
  Tissue = "",
  Outcome_name = "",
  add_info_cols = T,
  drop_non_heidi = T,
  hla = F,
  write_out = T
)

Arguments

smr_result_path

Character. The path containing SMR result file. Files should have the .smr extension.

writePath

Character. The path to write the adjusted results.

out_dir

Character. The output directory where adjusted files will be saved. If not specified, defaults to create a dir named fdr within dir-name (smr_result_path).

QTL_type

Character. The type of the QTL for SMR analysis.

Source

Character. The name of the Source.

Tissue

Character. The name of the Tissue.

Outcome_name

Character. The name of the Outcome.

add_info_cols

Logical. Whether to add information columns for: QTL_type, Source, Tissue and Outcome. Default is TRUE.

drop_non_heidi

Logical. Whether to drop Probes without HEIDI test information. Default is TRUE.

hla

Logical. Whether to pre-exclude the HLA region probes. Default is False.

write_out

Logical. Whether to write the adjusted results to a file. Default is TRUE.

Examples

if (FALSE) { # \dontrun{
leo_smr_adjust(
  file = "./output/smr-t2d/sqtl/GTEx49/chr_combined/chr_combine_sQTL_Adipose_Subcutaneous@iri3.smr",
  out_dir = "./output/smr-t2d/sqtl/GTEx49/fdr"
)
leo_smr_adjust(
  paste0("./output/smr-t2d/sqtl/GTEx49/chr_combined/",
         "chr_combine_sQTL_Adipose_Subcutaneous@iri3.smr"),
  writePath = "./haha.fdr", out_dir = ""
)
} # }