file_to_gwasvcf: Convert file(s) to gwasvcf format.

In jwr-git/mrpipeline: Implements a Ready-for-Use Mendelian Randomisation Pipeline

Convert file(s) to gwasvcf format.

Description

Function to convert a file (or files) to gwasvcf format.

Usage

file_to_gwasvcf(
  file,
  chr_col,
  pos_col,
  nea_col,
  ea_col,
  snp_col = NULL,
  eaf_col = NULL,
  beta_col = NULL,
  se_col = NULL,
  pval_col = NULL,
  n = NULL,
  n_case = NULL,
  name = NULL,
  header = TRUE,
  sep = "\t",
  cores = 1,
  bcf_tools = NULL,
  verbose = TRUE
)

Arguments

file	Path to file
chr_col	Column name for chromosome
pos_col	Column name for position
nea_col	Column name for non-effect allele
ea_col	Column name for effect allele
snp_col	Column name for SNP (Optional)
eaf_col	Column name for effect allele frequency (Optional)
beta_col	Column name for beta (Optional)
se_col	Column name for standard error (Optional)
pval_col	Column name for P value (Optional) NB: P values will be saved as 10^-P
n	Sample size (Optional), can be int or column name
n_case	Number of cases (Optional), can be int or column name
name	Trait name (Optional), can be string or column name
header	Whether file has a header or not (Optional, boolean)
sep	File separater (Optional)
cores	Number of cores for multi-threaded tasks (Optional) NB: Unavailable on Windows machines
bcf_tools	Path to bcf_tools (Optional)
verbose	Display verbose information (Optional, boolean)

Value

gwasvcf object(s)

See Also

[dat_to_gwasvcf()] for converting data.frames

jwr-git/mrpipeline documentation built on Oct. 2, 2022, 3:41 p.m.