read_prognosis: Read prognosis data

In Osmahmoud/SlopeHunter: Slope-Hunter: A ROBUST METHOD FOR COLLIDER BIAS CORRECTION IN CONDITIONAL GENOME-WIDE ASSOCIATION STUDIES

Read prognosis data

Description

Reads in prognosis data. Checks and organises columns for use with the Slope-Hunter analyses. Infers p-values when possible from beta and se.

Usage

read_prognosis(
  filename,
  snp_col = "SNP",
  beta_col = "BETA",
  se_col = "SE",
  pval_col = "PVAL",
  eaf_col = "EAF",
  effect_allele_col = "EA",
  other_allele_col = "OA",
  gene_col = "GENE",
  chr_col = "CHR",
  pos_col = "POS",
  min_pval = 1e-200,
  log_pval = FALSE
)

Arguments

filename	Filename. Must have header with at least the SNP, beta, se and EAcolumns present.
snp_col	Required name of column with SNP rs IDs. The default is "SNP".
beta_col	Required name of column with effect sizes. The default is "BETA".
se_col	Required name of column with standard errors. The default is "SE".
pval_col	Name of column with p-value (optional). The default is "PVAL". It will be Inferred when possible from beta and se.
eaf_col	Name of column with effect allele frequency (optional). The default is "EAF".
effect_allele_col	Required for harmonisation. Name of column with effect allele. Must be "A", "C", "T" or "G". The default is "EA".
other_allele_col	Required for harmonisation. Name of column with non-effect allele. Must be "A", "C", "T" or "G". The default is "OA".
gene_col	Optional column for gene name. The default is "GENE".
chr_col	Optional column for chromosome number. The default is "CHR".
pos_col	Optional column for SNP position. The default is "POS".
min_pval	Minimum allowed p-value. The default is 1e-200.
log_pval	The p-value is -log10(P). The default is FALSE.

Value

data frame

Osmahmoud/SlopeHunter documentation built on Oct. 7, 2022, 4:38 p.m.