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

read_outcome

R Documentation

Read outcomes

Description

Read a dataset (or datasets) as outcome. Can accept both OpenGWAS IDs or file paths. Accepts only gwasvcf file formats. This function can search for proxy SNPs locally, if supplied with the 'plink' and 'bfile' arguments. If these are not supplied, proxy searching will take place on the OpenGWAS servers only for OpenGWAS IDs. If you would like to search for proxies locally, please provide paths to Plink and bfiles.

Usage

read_outcome(
  ids,
  rsids,
  proxies = TRUE,
  proxy_rsq = 0.8,
  proxy_kb = 5000,
  proxy_nsnp = 5000,
  plink = NULL,
  bfile = NULL,
  cores = 1,
  cores_proxy = 1,
  verbose = TRUE
)

Arguments

`ids`	List of OpenGWAS IDs or file paths (to gwasvcf files)
`rsids`	List of SNP rsIDs to extract
`proxies`	Whether to search for proxies (Optional, boolean)
`proxy_rsq`	R2 threshold to use when searching for proxies (Optional)
`proxy_kb`	kb threshold to use when searching for proxies (Optional)
`proxy_nsnp`	Number of SNPs when searching for proxies (Optional)
`plink`	Path to Plink binary (Optional)
`bfile`	Path to Plink .bed/.bim/.fam files (Optional)
`cores`	Number of cores for multi-threaded tasks (Optional) NB: Unavailable on Windows machines
`cores_proxy`	Number of cores for multi-threaded proxy searching (Optional) NB: Unavailable on Windows machines NB: Should not be more than 'cores' argument!
`verbose`	Display verbose information (Optional, boolean)