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Attempt to perform MVMR using local data

Source: R/multivariable_mr.R
mv_extract_exposures_local.Rd

Allows you to read in summary data from text files to format the multivariable exposure dataset.

Usage

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,
  plink_bin = NULL,
  bfile = NULL,
  clump_r2 = 0.001,
  clump_kb = 10000,
  pop = "EUR",
  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=" ". If length is 1 it will use the same sep value for each exposure dataset. You can provide a vector of values, one for each exposure dataset, if the values are different across datasets. The same applies to all dataset-formatting options listed below.

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

plink_bin

If NULL and bfile is not NULL then will detect packaged plink binary for specific OS. Otherwise specify path to plink binary. Default = NULL

bfile

If this is provided then will use the API. Default = NULL

clump_r2

Default=0.001 for clumping

clump_kb

Default=10000 for clumping

pop

Which 1000 genomes super population to use for clumping when using the server

harmonise_strictness

See action argument in harmonise_data(). Default=2

Value

List

Details

Note that you can provide an array of column names for each column, which is of length filenames_exposure