Error when running COLOC
smsinks opened this issue · 2 comments
smsinks commented
Could you please help with the following error message.
I am attempting to execute COLOC on two GWAS summary statistics. However, when I try to run COLOC using the code provided below, an error is produced and displayed as follows:
> coloc_results <- coloc.abf(trait_eur_common,trait_afr_common, p1 = 1e-4, p2 = 1e-4)
Error in if (!(d$type %in% c("quant", "cc"))) stop("dataset ", suffix, :
the condition has length > 1
Below are the headers of the two data frames for the GWAS summary statistics:
head(trait_eur_common)
SNP beta varbeta p freq type
2 10:100090169_CTGCAGAAGA_C -2.622807 0.9998531 8.711e-03 0.21322 quant
25 10:101375113_CAA_C -3.900371 1.0001900 9.634e-05 0.86621 quant
30 10:10153657_TA_T 3.840330 1.0001721 1.232e-04 0.31934 quant
32 10:101662858_AT_A -5.319106 1.0000399 1.044e-07 0.45663 quant
39 10:101872090_GT_G -3.459913 0.9999495 5.400e-04 0.50672 quant
45 10:102617719_ACT_A 0.000000 0.0000000 1.745e-22 0.10627 quant
> head(trait_afr_common)
SNP beta varbeta p freq type
2 10:100090169_CTGCAGAAGA_C -2.903418 1.0002879 0.003701 0.032139 quant
25 10:101375113_CAA_C -2.613851 0.9998860 0.008945 0.757490 quant
30 10:10153657_TA_T -2.857322 1.0002255 0.004281 0.363300 quant
32 10:101662858_AT_A 2.597431 1.0003320 0.009416 0.577550 quant
39 10:101872090_GT_G 2.616783 0.9998343 0.008865 0.333510 quant
45 10:102617719_ACT_A 2.831188 1.0001328 0.004643 0.204350 quant
jeffreypullin commented
A more informative error is thrown by the current version of coloc:
Error in check_dataset(d = dataset1, 1) :
dataset 1: missing required element(s) snp
The error highlights the issue: the "SNP" column needs to be renamed to "snp".
chr1swallace commented
The dataset is supposed to be a list, not a data frame. There should be a single value for type, not one for each SNP. This is to emphasise that type is a study level, not snp level variable
…________________________________
From: catheriz ***@***.***>
Sent: Sunday, December 17, 2023 2:53:46 AM
To: chr1swallace/coloc ***@***.***>
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Subject: Re: [chr1swallace/coloc] Error when running COLOC (Issue #117)
same error:
Error in if (!(d$type %in% c("quant", "cc"))) stop("dataset ", suffix, :
the condition has length > 1
My data looks like this:
snp chromosome position allele1 allele2 maf
35112 1:113709948:T:C 1 113709948 C T 0.017673257
485129 1:113710657:G:T 1 113710657 T G 0.008543363
617108 1:113710779:C:T 1 113710779 T C 0.008247302
36097 1:113710928:G:A 1 113710928 A G 0.017593139
10906 1:113711017:C:T 1 113711017 T C 0.248750745
10822 1:113711270:A:G 1 113711270 G A 0.250942147
beta se z N varbeta type
35112 -0.591678 0.2111050 -2.8027664 12791 0.044565321 cc
485129 0.240849 0.2486460 0.9686422 12791 0.061824833 cc
617108 0.187615 0.2451400 0.7653382 12791 0.060093620 cc
36097 -0.587967 0.2112820 -2.7828542 12791 0.044640084 cc
10906 -0.233390 0.0506506 -4.6078428 12791 0.002565483 cc
10822 -0.235175 0.0506890 -4.6395668 12791 0.002569375 cc
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