Run GCTA-COJO

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.

Usage

Arguments

Value

See also