COJO_args: COJO arguments

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

COJO arguments

Description

COJO arguments, with documentation from the GCTA website.

Usage

COJO_args(
  cojo_file,
  bfile,
  out,
  cojo_slct = NULL,
  cojo_cond = NULL,
  cojo_joint = NULL,
  thread_num = NULL,
  maf = NULL,
  max_maf = NULL,
  exclude = NULL,
  cojo_top_SNPs = NULL,
  cojo_p = NULL,
  cojo_wind = NULL,
  cojo_collinear = NULL,
  diff_freq = NULL,
  cojo_gc = NULL,
  ...
)

Arguments

cojo_file	Input the summary-level statistics from a meta-analysis GWAS (or a single GWAS).
bfile	Input PLINK binary PED files, e.g. test.fam, test.bim and test.bed (see PLINK user manual for details).
out	Specify output root filename.
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.
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.
exclude	Specify a list of SNPs to be excluded from the analysis.
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.
...	Additional arguments to be passed directly to GCTA-COJO (as character strings).

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