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

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
)

## Arguments

filename Filename. Must have header with at least SNP column present. SNPs to extract. If NULL, which the default, then doesn't extract any and keeps all. Specify delimeter in file. The default is space, i.e. sep=" ". 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". Required name of column with SNP rs IDs. The default is "SNP". Required for MR. Name of column with effect sizes. THe default is "beta". Required for MR. Name of column with standard errors. The default is "se". Required for MR. Name of column with effect allele frequency. The default is "eaf". Required for MR. Name of column with effect allele. Must be "A", "C", "T" or "G". The default is "effect_allele". Required for MR. Name of column with non effect allele. Must be "A", "C", "T" or "G". The default is "other_allele". Required for enrichment tests. Name of column with p-value. The default is "pval". Optional column name for units. The default is "units". Optional column name for number of cases. The default is "ncase". Optional column name for number of controls. The default is "ncontrol". Optional column name for sample size. The default is "samplesize". Optional column name for gene name. The default is "gene". 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". Minimum allowed p-value. The default is 1e-200. The pval is -log10(P). The default is FALSE.

data frame