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Here is my code for this susie-coloc, but the ld matrix seems a bit unusual as indicated by warning from susie:
In susie_suff_stat(XtX = XtX, Xty = Xty, n = n, yty = (n - 1) * :
IBSS algorithm did not converge in 100 iterations!
Please check consistency between summary statistics and LD matrix.
See https://stephenslab.github.io/susieR/articles/susierss_diagnostic.html
my code
x = out[[1]]
x = as.data.frame(x) # list can trans into a matrix directly but df would be just fine
# dim(x)
colnames(x)
x = TwoSampleMR::format_data(x, type = "exposure",
# phenotype_col = "Phenotype",
snp_col = "snp",
chr_col = "chr",
pos_col = "position",
effect_allele_col = "A1",
other_allele_col = "A2",
# eaf_col = "EAF",
beta_col = "beta",
# se_col = "SE",
pval_col = "pvalues",
min_pval = 1e-400
)
ld <- ieugwasr::ld_matrix_local(
x$SNP,
bfile = bfile,
plink_bin = plinkbinr::get_plink_exe(),
with_alleles = T
)
x2 = harmonise_ld_dat(x, ld)
susie_fit = susie_rss(x2$x$z.exposure, x2$ld, n=500) # unusual result, can not converge
The text was updated successfully, but these errors were encountered:
laleoarrow
changed the title
oloc
Anyone use this to calculate LD matrix for coloc-susie? Is there a bug in ld_matrix_local?
Apr 16, 2024
Here is my code for this susie-coloc, but the ld matrix seems a bit unusual as indicated by warning from susie:
my code
The text was updated successfully, but these errors were encountered: