COJO_run: Run _GCTA-COJO_

In RajLabMSSM/echofinemap: echoverse module: Fine-mapping functions

Run GCTA-COJO

Description

Run GCTA-COJO.

Usage

COJO_run(
  gcta_path,
  bfile,
  cojo_slct = TRUE,
  cojo_cond = TRUE,
  cojo_joint = FALSE,
  conditioned_snps = NULL,
  prefix = "cojo",
  cojo_dir,
  cojo_file = file.path(cojo_dir, paste0(prefix, ".file.ma")),
  exclude = file.path(cojo_dir, "excluded_snps.txt"),
  verbose = TRUE,
  ...
)

Arguments

gcta_path	Path to the GCTA-COJO executable.
bfile	Input PLINK binary PED files, e.g. test.fam, test.bim and test.bed (see PLINK user manual for details).
cojo_slct	Perform a stepwise model selection procedure to select independently associated SNPs. Results will be saved in a *.jma file with additional file *.jma.ldr showing the LD correlations between the SNPs.
cojo_cond	Perform association analysis of the included SNPs conditional on the given list of SNPs. Results will be saved in a *.cma. The conditional SNP effects (i.e. bC) will be labelled as "NA" if the multivariate correlation between the SNP in question and all the covariate SNPs is > 0.9.
cojo_joint	Fit all the included SNPs to estimate their joint effects without model selection. Results will be saved in a *.jma file with additional file *.jma.ldr showing the LD correlations between the SNPs.
conditioned_snps	Which SNPs to conditions on when fine-mapping with (e.g. COJO).
prefix	Prefix to use for file names.
cojo_dir	Directory to store results in.
cojo_file	Input the summary-level statistics from a meta-analysis GWAS (or a single GWAS).
exclude	Specify a list of SNPs to be excluded from the analysis.
verbose	Print messages.
...	Arguments passed on to COJO_args out Specify output root filename. maf Exclude SNPs with minor allele frequency (MAF) less than a specified value, e.g. 0.01. max_maf Include SNPs with MAF less than a specified value, e.g. 0.1. cojo_top_SNPs Perform a stepwise model selection procedure to select a fixed number of independently associated SNPs without a p-value threshold. The output format is the same as that from --cojo-slct. cojo_p Threshold p-value to declare a genome-wide significant hit. The default value is 5e-8 if not specified. This option is only valid in conjunction with the option --cojo-slct. Note: it will be extremely time-consuming if you set a very low significance level, e.g. 5e-3. cojo_wind Specify a distance d (in Kb unit). It is assumed that SNPs more than d Kb away from each other are in complete linkage equilibrium. The default value is 10000 Kb (i.e. 10 Mb) if not specified. cojo_collinear During the model selection procedure, the program will check the collinearity between the SNPs that have already been selected and a SNP to be tested. The testing SNP will not be selected if its multiple regression R2 on the selected SNPs is greater than the cutoff value. By default, the cutoff value is 0.9 if not specified. diff_freq To check the difference in allele frequency of each SNP between the GWAS summary datasets and the LD reference sample. SNPs with allele frequency differences greater than the specified threshold value will be excluded from the analysis. The default value is 0.2. cojo_gc If this option is specified, p-values will be adjusted by the genomic control method. By default, the genomic inflation factor will be calculated from the summary-level statistics of all the SNPs unless you specify a value, e.g. --cojo-gc 1.05.

Value

Input and output file paths.

See Also

Other COJO: COJO_locus_subdir(), COJO_process_results(), COJO()

RajLabMSSM/echofinemap documentation built on Jan. 3, 2023, 1:42 a.m.