arguments imply differing number of rows

[bujnism]

Hello,

I have a list of phenotype exposures I am testing against my outcome of interest from my GWAS data. I am able to run MR PRESSO when I use the GWAS as the exposure, but not as outcome. The error message seems to be suggesting that it is due to the row numbers not being the same, but I don't see what the problem is with the input. It also runs most of the way.

I am running MR PRESSO within the TwoSampleMR package, but they do not offer any advice on using it. Have you seen this error before or possibly have any insight into this? Is it just indeed there are no outliers, or is that because of some error within the data?

Any advice would be greatly appreciated!

command: resPRESSO<-run_mr_presso(dat_HToutcome,NbDistribution = 10000)

output: Intelligence || id:ebi-a-GCST006250 - outcome systolic blood pressure || id:ieu-b-38 - outcome Alzheimer's disease || id:ieu-b-2 - outcome Celiac disease || id:ebi-a-GCST005523 - outcome HDL cholesterol || id:ieu-b-109 - outcome Height || id:ieu-a-89 - outcome Coronary heart disease || id:ieu-a-9 - outcome diastolic blood pressure || id:ieu-b-39 - outcome Rheumatoid arthritis || id:ebi-a-GCST90013534 - outcome Sporadic miscarriage || id:ebi-a-GCST011888 - outcome Schizophrenia || id:ieu-b-5070 - outcome apolipoprotein A-I || id:ieu-b-107 - outcome Ankylosing spondylitis || id:ebi-a-GCST005529 - outcome triglycerides || id:ieu-b-111 - outcome Heart rate || id:ieu-a-1056 - outcome Atrial fibrillation || id:ebi-a-GCST006414 - outcome Autism Spectrum Disorder || id:ieu-a-1185 - outcome apolipoprotein B || id:ieu-b-108 - outcome bipolar disorder || id:ieu-b-41 - outcome multiple sclerosis || id:ieu-b-18 - outcome Depression (broad) || id:ebi-a-GCST005902 - outcome body mass index || id:ieu-b-40 - outcome Sarcoidosis (non-Lofgren's syndrome) || id:ebi-a-GCST005543 - outcome Psoriasis || id:ebi-a-GCST90019017 - outcome Fasting glucose || id:ebi-a-GCST90002232 - outcome Juvenile idiopathic arthritis (oligoarticular or rheumatoid factor-negative polyarticular) || id:ebi-a-GCST005528 - outcome Major depression || id:ieu-b-102 - outcome WARNING: MR-PRESSO failed for Intelligence || id:ebi-a-GCST006250 systolic blood pressure || id:ieu-b-38 Alzheimer's disease || id:ieu-b-2 Celiac disease || id:ebi-a-GCST005523 HDL cholesterol || id:ieu-b-109 Height || id:ieu-a-89 Coronary heart disease || id:ieu-a-9 diastolic blood pressure || id:ieu-b-39 Rheumatoid arthritis || id:ebi-a-GCST90013534 Sporadic miscarriage || id:ebi-a-GCST011888 Schizophrenia || id:ieu-b-5070 apolipoprotein A-I || id:ieu-b-107 Ankylosing spondylitis || id:ebi-a-GCST005529 triglycerides || id:ieu-b-111 Heart rate || id:ieu-a-1056 Atrial fibrillation || id:ebi-a-GCST006414 Autism Spectrum Disorder || id:ieu-a-1185 apolipoprotein B || id:ieu-b-108 bipolar disorder || id:ieu-b-41 multiple sclerosis || id:ieu-b-18 Depression (broad) || id:ebi-a-GCST005902 body mass index || id:ieu-b-40 Sarcoidosis (non-Lofgren's syndrome) || id:ebi-a-GCST005543 Psoriasis || id:ebi-a-GCST90019017 Fasting glucose || id:ebi-a-GCST90002232 Juvenile idiopathic arthritis (oligoarticular or rheumatoid factor-negative polyarticular) || id:ebi-a-GCST005528 Major depression || id:ieu-b-102 Heel bone mineral density || id:ebi-a-GCST006979 Sjogren's syndrome (SPA correction) || id:ebi-a-GCST90013929 HbA1C || id:ieu-b-103 Systemic lupus erythematosus || id:ebi-a-GCST90011866 Chronic gastritis || id:ebi-a-GCST90018825 LDL cholesterol || id:ieu-b-110 Type 1 diabetes || id:ebi-a-GCST90000529 Myocardial infarction || id:ieu-a-798 Ulcerative colitis || id:ieu-a-970 Cardiovascular disease || id:ebi-a-GCST90038595 Heart failure || id:ebi-a-GCST009541 Sarcoidosis (Lofgren's syndrome) || id:ebi-a-GCST005540 Total cholesterol || id:ieu-a-301 Triglycerides || id:ieu-a-302 Type 2 diabetes || id:ebi-a-GCST006867 Type 2 diabetes (adjusted for BMI) || id:ebi-a-GCST007518 -> outcome <simpleError in data.frame(..., check.names = FALSE): arguments imply differing number of rows: 1, 0> Warning messages: 1: In MRPRESSO::mr_presso(BetaOutcome = "beta.outcome", BetaExposure = "beta.exposure", : No outlier were identified, therefore the results for the outlier-corrected MR are set to NA 2: In MRPRESSO::mr_presso(BetaOutcome = "beta.outcome", BetaExposure = "beta.exposure", : No outlier were identified, therefore the results for the outlier-corrected MR are set to NA 3: In MRPRESSO::mr_presso(BetaOutcome = "beta.outcome", BetaExposure = "beta.exposure", : No outlier were identified, therefore the results for the outlier-corrected MR are set to NA 4: In MRPRESSO::mr_presso(BetaOutcome = "beta.outcome", BetaExposure = "beta.exposure", : No outlier were identified, therefore the results for the outlier-corrected MR are set to NA 5: In MRPRESSO::mr_presso(BetaOutcome = "beta.outcome", BetaExposure = "beta.exposure", : No outlier were identified, therefore the results for the outlier-corrected MR are set to NA 6: In MRPRESSO::mr_presso(BetaOutcome = "beta.outcome", BetaExposure = "beta.exposure", : No outlier were identified, therefore the results for the outlier-corrected MR are set to NA 7: In MRPRESSO::mr_presso(BetaOutcome = "beta.outcome", BetaExposure = "beta.exposure", : No outlier were identified, therefore the results for the outlier-corrected MR are set to NA 8: In MRPRESSO::mr_presso(BetaOutcome = "beta.outcome", BetaExposure = "beta.exposure", : No outlier were identified, therefore the results for the outlier-corrected MR are set to NA

[bujnism]

Also, it errors at 27/41 of the input phenotypes to test. so it does not finish the run but gets quite far.

[YuHao0099]

Hi, @bujnism Have you solved this problem yet? I met with the same problem when running mr_presso( ) after harmonising data. Thanks.