chr1swallace / coloc

Repo for the R package coloc

chr1swallace/coloc Issues

Consider adding reference to SuSiE sumstats paper
Updated 19 days ago
coloc.abf error
Closed 8 months ago4
error for coloc input datacheck
Updated 2 months ago
Why is the PP.H4.abf result of res$summary different from the maximum PP.H4 in res$results?
Updated 2 months ago3
Question about Using `Effective Sample Size` vs `Observed Sample Size` for Coloc Analysis
Updated 2 months ago
GWAS-GWAS colocalisation
Updated 2 months ago6
coloc.abf result: unexpectedly high PP.H4.abf
Updated 3 months ago4
runsusie() error with convergence
Updated 3 months ago1
The minimum number of specific gene eQTLs included in the COLOC analysis?
Closed 3 months ago
coloc.abf and check_dataset returen "missing value where TRUE/FALSE needed"
Updated 4 months ago1
runsusie and susieR results differ
Updated 4 months ago8
Error in coloc.susie ()
Updated 4 months ago2
coloc.susie returns NA results without error message
Closed 4 months ago3
NULL Result from coloc.susie
Updated 4 months ago
Is the distribution of effect size estimates specifically and strictly required to follow Normal Distribution?
Updated 4 months ago
How are representative hits chosen in results summary table?
Updated 4 months ago
How to interpret the results of susie summary？
Updated 4 months ago3
The pre-process of QTL-GWAS colocalisation
Updated 4 months ago3
LD matrix on SuSIE_coloc
Closed 10 months ago7
"cc" and "quant" variables effect size
Closed 5 months ago2
Add quiet=FALSE to coloc.abf()
Updated 5 months ago
[Question] Calculating coloc.abf PP.H4.abf
Closed 6 months ago
Error when running `check_dataset()`
Closed 6 months ago3
Error if beta and/or varbeta contain `Inf`
Closed 7 months ago5
Error when running check_dataset
Updated 7 months ago1
Error when running COLOC
Updated 8 months ago2
Setting per-SNP priors to maintain per-hypothesis priors when number of SNPs is large?
Updated 9 months ago
Warning messages:1: In adjust_prior(p1, nrow(df1), "1") : p1 * nsnps >= 1, setting p1=1/(nsnps + 1)；2: In adjust_prior(p2, nrow(df2), "2") : p2 * nsnps >= 1, setting p2=1/(nsnps + 1)
Updated 9 months ago
Summary stats of two traits are from the same dataset
Closed 9 months ago6
XtX is not symmetric
Closed 9 months ago1
description errors
Updated 9 months ago
coloc.abf
Updated 10 months ago1
Question on "First: select the SNPs to study."
Updated a year ago
How to determine N for runsusie (each SNP with different N value)
Updated a year ago
length of snp vector should be 1 less than ncol(res$lbf_variable)
Updated a year ago6
error in check_dataset: duplicated SNPs
Updated a year ago4
runsusie error report: Error in (function (z, R, n, bhat, shat, var_y, z_ld_weight = 0, estimate_residual_variance = FALSE, : The dimension of R (0 x 0) does not agree with expected (500 x 500)
Updated a year ago2
object 'LD' not found in installation (build_vignettes=TRUE)
Updated a year ago4
Query about eQTL summary selection for coloc analysis
Updated a year ago
Summary from coloc.susie is missing pairwise comparisons between credible sets?
Updated a year ago
coloc.susie detected high PP.H4.abf but the result does not make sense
Updated a year ago
coloc error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) :NA/NaN/Inf in 'x'
Updated a year ago
Sample size (N or n) not recognised by coloc.susie
Closed a year ago1
prepare the data structure for coloc.abf and loop for multiple variants running together
Updated a year ago
Results from coloc.abf
Updated a year ago3
Questions about the coloc hypotheses
Updated a year ago
How to construct a dataset for coloc analysis?
Closed a year ago6
Colocalization of eQTL and GWAS
Updated a year ago5
Interpretation on SNP.PP.H4
Updated 2 years ago2
Using coloc for conditionally independent eQTLs in the HLA region
Updated 2 years ago3