Under construction

mv_extract_exposures_local(
  filenames_exposure,
  sep = " ",
  phenotype_col = "Phenotype",
  snp_col = "SNP",
  beta_col = "beta",
  se_col = "se",
  eaf_col = "eaf",
  effect_allele_col = "effect_allele",
  other_allele_col = "other_allele",
  pval_col = "pval",
  units_col = "units",
  ncase_col = "ncase",
  ncontrol_col = "ncontrol",
  samplesize_col = "samplesize",
  gene_col = "gene",
  id_col = "id",
  min_pval = 1e-200,
  log_pval = FALSE,
  pval_threshold = 5e-08,
  clump_r2 = 0.001,
  clump_kb = 10000,
  harmonise_strictness = 2
)

Arguments

filenames_exposure

Filenames for each exposure dataset. Must have header with at least SNP column present. Following arguments are used for determining how to read the filename and clumping etc.

sep

Specify delimeter in file. The default is space, i.e. sep=" ".

phenotype_col

Optional column name for the column with phenotype name corresponding the the SNP. If not present then will be created with the value "Outcome". Default is "Phenotype".

snp_col

Required name of column with SNP rs IDs. The default is "SNP".

beta_col

Required for MR. Name of column with effect sizes. THe default is "beta".

se_col

Required for MR. Name of column with standard errors. The default is "se".

eaf_col

Required for MR. Name of column with effect allele frequency. The default is "eaf".

effect_allele_col

Required for MR. Name of column with effect allele. Must be "A", "C", "T" or "G". The default is "effect_allele".

other_allele_col

Required for MR. Name of column with non effect allele. Must be "A", "C", "T" or "G". The default is "other_allele".

pval_col

Required for enrichment tests. Name of column with p-value. The default is "pval".

units_col

Optional column name for units. The default is "units".

ncase_col

Optional column name for number of cases. The default is "ncase".

ncontrol_col

Optional column name for number of controls. The default is "ncontrol".

samplesize_col

Optional column name for sample size. The default is "samplesize".

gene_col

Optional column name for gene name. The default is "gene".

id_col

Optional column name to give the dataset an ID. Will be generated automatically if not provided for every trait / unit combination. The default is "id".

min_pval

Minimum allowed p-value. The default is 1e-200.

log_pval

The pval is -log10(P). The default is FALSE.

pval_threshold

Default=5e-8 for clumping

clump_r2

Default=0.001 for clumping

clump_kb

Default=10000 for clumping

harmonise_strictness

See action argument in harmonise_data. Default=2

Value

List