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chr1swallace / coloc

Repo for the R package coloc
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Error in coloc.susie () #160

Open Huiflorazhan opened 2 months ago

Huiflorazhan commented 2 months ago

I use PLINK to generate LD matrix and then try to run coloc.susie(), but I got this error. Could you please help me with it? Thank you for your time.

susie.res <- coloc.susie(list1, list2)

Error message:

running max iterations: 100
Error in if (n <= 1) stop("n must be greater than 1") : 
  the condition has length > 1
In addition: Warning message:
In check_dataset(d, suffix, req = c("beta", "varbeta", "LD", "snp",  :
  minimum p value is: 6.673e-05
If this is what you expected, this is not a problem.
If this is not as small as you expected, please check you supplied var(beta) and not sd(beta) for the varbeta argument. If that's not the explanation, please check the 02_data vignette.
chr1swallace commented 2 months ago

I can't help unless you show me what your input data looks like

-- https://chr1swallace.github.io

From: Huiflorazhan @.> Sent: Friday, April 12, 2024 2:52:03 AM To: chr1swallace/coloc @.> Cc: Subscribed @.***> Subject: [chr1swallace/coloc] Error in coloc.susie () (Issue #160)

I use PLINK to generate LD matrix and then try to run coloc.susie(), but I got this error. Could you please help me with it? Thank you for your time.

susie.res <- coloc.susie(list1, list2)

Error message:

running max iterations: 100 Error in if (n <= 1) stop("n must be greater than 1") : the condition has length > 1 In addition: Warning message: In check_dataset(d, suffix, req = c("beta", "varbeta", "LD", "snp", : minimum p value is: 6.673e-05 If this is what you expected, this is not a problem. If this is not as small as you expected, please check you supplied var(beta) and not sd(beta) for the varbeta argument. If that's not the explanation, please check the 02_data vignette.

— Reply to this email directly, view it on GitHubhttps://github.com/chr1swallace/coloc/issues/160, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAQWR2EEGECSPMCRE4N4ENDY4444HAVCNFSM6AAAAABGDJTRG2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGIZTQOBYG4YDSNQ. You are receiving this because you are subscribed to this thread.Message ID: @.***>

Huiflorazhan commented 2 months ago

I can't help unless you show me what your input data looks like … -- https://chr1swallace.github.io ____ From: Huiflorazhan @.> Sent: Friday, April 12, 2024 2:52:03 AM To: chr1swallace/coloc @.> Cc: Subscribed @.> Subject: [chr1swallace/coloc] Error in coloc.susie () (Issue #160) I use PLINK to generate LD matrix and then try to run coloc.susie(), but I got this error. Could you please help me with it? Thank you for your time. susie.res <- coloc.susie(list1, list2) Error message: running max iterations: 100 Error in if (n <= 1) stop("n must be greater than 1") : the condition has length > 1 In addition: Warning message: In check_dataset(d, suffix, req = c("beta", "varbeta", "LD", "snp", : minimum p value is: 6.673e-05 If this is what you expected, this is not a problem. If this is not as small as you expected, please check you supplied var(beta) and not sd(beta) for the varbeta argument. If that's not the explanation, please check the 02_data vignette. — Reply to this email directly, view it on GitHub<#160>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAQWR2EEGECSPMCRE4N4ENDY4444HAVCNFSM6AAAAABGDJTRG2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGIZTQOBYG4YDSNQ. You are receiving this because you are subscribed to this thread.Message ID: @.>

The input data like this

image image image