read_outcome_data: Read outcome data

In MRCIEU/TwoSampleMR: Two Sample MR Functions and Interface to MR Base Database

Read outcome data

Description

Reads in outcome data. Checks and organises columns for use with MR or enrichment tests. Infers p-values when possible from beta and se.

Usage

read_outcome_data(
  filename,
  snps = NULL,
  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,
  chr_col = "chr",
  pos_col = "pos"
)

Arguments

filename	Filename. Must have header with at least SNP column present.
snps	SNPs to extract. If NULL, which the default, then doesn't extract any and keeps all.
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.
chr_col	Optional column name for chromosome. Default is "chr".
pos_col	Optional column name for genetic position Default is "pos".

Value

data frame

MRCIEU/TwoSampleMR documentation built on Sept. 28, 2024, 6:51 p.m.