Diagnose LD mismatch using SuSiE RSS
Usage
diagnose_LD_mismatch_susie(
region_ids,
z_snp,
LD_map,
gwas_n,
p_diff_thresh = 5e-06,
plot = TRUE,
LD_format = c("rds", "rdata", "mtx", "csv", "txt", "custom"),
LD_loader_fun = NULL,
snpinfo_loader_fun = NULL,
ncore = 1,
logfile = NULL
)Arguments
- region_ids
A vector of region IDs to run diagnosis
- z_snp
A data frame with two columns: "id", "A1", "A2", "z". giving the z scores for snps. "A1" is effect allele. "A2" is the other allele.
- LD_map
a data frame with filenames of LD matrices and SNP information for each of the regions.
- gwas_n
integer, GWAS sample size.
- p_diff_thresh
numeric, p-value cutoff for identifying problematic SNPs with significant difference between observed z-scores and estimated values.
- plot
If TRUE, plot observed z score vs the expected value.
- LD_format
file format for LD matrix. If "custom", use a user defined
LD_loader_fun()function to load LD matrix.- LD_loader_fun
a user defined function to load LD matrix when
LD_format = "custom".- snpinfo_loader_fun
a user defined function to load SNP information file, if SNP information files are not in standard cTWAS reference format.
- ncore
integer, number of cores for parallel computing.
- logfile
the log file, if NULL will print log info on screen