construct_colmap: Target column map

In RajLabMSSM/echodata: echoverse module: Fine-mapping data access and formatting

Target column map

Description

This function wraps all column name mappings for the full GWAS/QTL summary statistics file specified by fullSS_path (i.e. the "target").

Usage

construct_colmap(
  munged = FALSE,
  CHR = "CHR",
  POS = "POS",
  SNP = "SNP",
  P = "P",
  Effect = "Effect",
  StdErr = "StdErr",
  tstat = "tstat",
  Locus = "Locus",
  Freq = "Freq",
  MAF = "MAF",
  A1 = "A1",
  A2 = "A2",
  Gene = "Gene",
  N_cases = "N_cases",
  N_controls = "N_controls",
  proportion_cases = "calculate",
  N = "N",
  verbose = TRUE
)

Arguments

munged	Whether fullSS_path have already been standardised/filtered full summary stats with format_sumstats. If munged=FALSE you'll need to provide the necessary column names to the colmap argument.
CHR	Name of the chromosome column in the full summary stats file. Can be "chr1" or "1" format. (default: ="CHR")
POS	Name of the genomic position column in the full summary stats file. Must be in units of basepairs. (default: ="POS")
SNP	Name of the SNP RSID column in the full summary stats file. (default: ="SNP")
P	Name of the p-value column in the full summary stats file. Raw p-values are preferred, but if not available corrected p-values (e.g. FDR) can be used instead. (default: ="P")
Effect	Name of the effect size column in the full summary stats file. Effect size is preferred, but if not available other metrics like Beta for Odds Ratio can be used instead. (default: ="Effect")
StdErr	Name of the standard error column in the full summary stats file. You can also set stderr="calculate" to infer standard error using: effect / tstat. (default: ="StdErr")
tstat	Name of the t-statistic column in the full summary stats file. This column is not necessary unless stderr="calculate" or the standard error column is missing. (default: ="t-stat")
Locus	Name of the locus column in the full summary stats file. (default: ="Locus")
Freq	Name of the allele frequency column in the full summary stats file. Effect allele frequency is preferred, but the non-effect allele can be provided instead (though this may be less accurate). This column is not necessary unless MAF="calculate" or the MAF column is missing. (default: ="Freq")
MAF	Name of the minor allele frequency column in the full summary stats file. Can be inferred from freq if missing from the dataset. (default: ="MAF")
A1	Name of the effect/risk allele column in the full summary stats.
A2	Name of the other/non-risk allele column in the full summary stats.
Gene	For QTL studies, the name of the \[e\]gene column in the full summary stats file (default: "gene"). This column will be used for filtering summary stats if supplying a named list of gene:Locus pairs to loci.
N_cases	The number of case subjects in the study. Instead of providing a redundant N_cases column, you can simply enter one value here.
N_controls	The number of control subjects in the study. Instead of providing a redundant N_controls column, you can simply enter one value here.
proportion_cases	The proportion of total subjects in the study that were cases. if proportion_cases="calculate" then this is inferred: N_controls / N_controls.
N	Name of the column containing the total sample size.
verbose	Print messages.

Examples

colmap <- echodata::construct_colmap(munged=TRUE)

RajLabMSSM/echodata documentation built on Nov. 21, 2023, 8 a.m.