lhc_mr: Main trait pair analysis using LHC-MR

In LizaDarrous/lhcMR: Latent Heritable Confounder - Mendelian Randomisation

Main trait pair analysis using LHC-MR

Description

Main trait pair analysis using LHC-MR

Usage

lhc_mr(
  SP_list,
  trait.names,
  partition = NA,
  account = NA,
  param = "comp",
  paral_method = "rslurm",
  nCores = NA,
  nBlock = 200,
  M = 1e+07
)

Arguments

SP_list	List resulting from calculate_SP. Contains the filtered dataset (by every 'SNP_filter'th SNP), the starting points to be used in the pair trait optimisation, the traits' intercepts, the traits' polygenicity if nStep = 2, as well as some extra parameters like the cross-trait intercept and bidirectional causal effect estimated by IVW
trait.names	Vector containing the trait names in the order they were used in merge_sumstats(): Exposure, Outcome
partition	String indicating the partition name to be used for the "rslurm" parallelisation - equivalent to '-p, –partition' in SLURM commands
account	String indicating the account name to be used for the "rslurm" parallelisation - equivalent to '-A, –account' in SLURM commands
param	String indicating which model the likelihood function will be optimised with, either "comp" by default or "U" for a no-confounder model
paral_method	String indicating which method to parallelise the optimisation over the number of sets of starting points. "rslurm" will submit the calculation to a SLURM cluster using a 'Slurm' workload manager, "lapply" will parallelise the optimisation using 'mclapply' over a set number of cores but will go sequentially over the sets of starting points and thus take more time.
nCores	Numerical value indicating number of cores to be used in 'mclapply' to parallelise the analysis. If not set (default value = NA), then it will be calculated as 2/3 of the available cores
nBlock	Numerical value indicating the number of blocks to create from the block jackknife analysis, where at each iteration one block is left out and the optimisation is ran again for a single starting point to obtain eventually 'nBlock' estimates and calculate the SE of the parameter estimates
M	Numerical value indicating the number of SNPs used to calculate the LD reported in the LD file (for genotyped SNPs). Default value = 1e7

Value

Prints out a summary of the results

LizaDarrous/lhcMR documentation built on March 24, 2024, 10:28 p.m.