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Error in check.dataset(dataset, "") : dataset : sample size N not set #2

Open Shabs86 opened 3 years ago

Shabs86 commented 3 years ago

I ran this and got: Error in check.dataset(dataset, "") : dataset : sample size N not set. I am not sure what I am doing wrong here. I do use the correct value of token retrieved from LDlink site.

CONQUER::summarize(variants = c("rs192335285","rs191238524","rs635634","rs139988391","rs201955556") , directory=getwd(),multiAnalyze=TRUE, token="VALUE", population = "FIN",tissues=tissues_list)

0 variants are already present, 5 to be done Retrieving data for: rs192335285 getVariantInfoEnsembl getLDLink getChromatinInteractionData geteQTLdata Gene expression rs192335285 successful! Retrieving data for: rs191238524 getVariantInfoEnsembl getLDLink getChromatinInteractionData geteQTLdata Gene expression rs191238524 successful! Retrieving data for: rs635634 getVariantInfoEnsembl getLDLink getChromatinInteractionData geteQTLdata Gene expression rs635634 successful! Retrieving data for: rs139988391 getVariantInfoEnsembl getLDLink Reverting to ENSEMBL:rs59419587 is not in 1000G reference panel.getChromatinInteractionData geteQTLdata Gene expression rs139988391 successful! Retrieving data for: rs201955556 getVariantInfoEnsembl getLDLink getChromatinInteractionData geteQTLdata Gene expression rs201955556 successful! Colocalization has not yet been performed. Note that this may take time some time depending on the number of SNPs. Running.. rs192335285 rs191238524 rs635634 Error in check.dataset(dataset, "") : dataset : sample size N not set

roderickslieker commented 3 years ago

Hi,

Thank you for your feedback. I cannot reproduce the error on R-4.0.3? Perhaps you can re-run the code on R-4.0.3?

Roderick

Shabs86 commented 3 years ago

Thanks for your quick reply! I am running 4.0.3 version of R.

> version _
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 4
minor 0.3
year 2020
month 10
day 10
svn rev 79318
language R
version.string R version 4.0.3 (2020-10-10) nickname Bunny-Wunnies Freak Out

roderickslieker commented 3 years ago

Hi I cannot reproduce the error. Did you typed the tissue name wrong perhaps? See conquer.db::gtexTissuesV8

Roderick

Shabs86 commented 3 years ago

So, I used tissues_list=conquer.db::gtexTissuesV8, as I wanted to see which all tissues those snps expressed onto. Is this the reason why it's giving that error? Or could it be that the snps are not in databases?

roderickslieker commented 3 years ago

Hi,

Can you try to re-run without specifying your tissues. It will take them all automatically.

CONQUER::summarize(variants = c("rs192335285","rs191238524","rs635634","rs139988391","rs201955556") , directory=getwd(),multiAnalyze=TRUE, token="VALUE", population = "FIN")

You can keep the snp files in the folders, they are fine and independent from the colocalization

Shabs86 commented 3 years ago

So, I re-ran in accordance with how you said this after deleting history/env/.Rdata, so that it can start afresh. It still ends with saying Error in dataset and visualise doesn't show any coloc analysis

CONQUER::summarize(variants = snps ,directory=getwd(),multiAnalyze=TRUE,token='VALUE',population = "FIN") 0 variants are already present, 5 to be done Retrieving data for: rs192335285 getVariantInfoEnsembl getLDLink getChromatinInteractionData geteQTLdata Gene expression rs192335285 successful! Retrieving data for: rs191238524 getVariantInfoEnsembl getLDLink getChromatinInteractionData geteQTLdata Gene expression rs191238524 successful! Retrieving data for: rs635634 getVariantInfoEnsembl getLDLink getChromatinInteractionData geteQTLdata Gene expression rs635634 successful! Retrieving data for: rs139988391 getVariantInfoEnsembl getLDLink Reverting to ENSEMBL:rs59419587 is not in 1000G reference panel.getChromatinInteractionData geteQTLdata Gene expression rs139988391 successful! Retrieving data for: rs201955556 getVariantInfoEnsembl getLDLink getChromatinInteractionData geteQTLdata Gene expression rs201955556 successful! Colocalization has not yet been performed. Note that this may take time some time depending on the number of SNPs. Running.. rs192335285 rs191238524 rs635634 Error in check.dataset(dataset, "") : dataset : sample size N not set In addition: There were 50 or more warnings (use warnings() to see the first 50)

roderickslieker commented 3 years ago

OK this is all very weird because I cannot reproduce. Can you try this:

x <- CONQUER:::getColocalization("rs635634") dim(x) head(x)

Shabs86 commented 3 years ago

Yeah it is indeed a strange issue! I re-ran what you suggested and this is the output:

x <- CONQUER:::getColocalization("rs635634") rs635634 Error in check.dataset(dataset, "") : dataset : sample size N not set dim(x) Error: object 'x' not found head(x) Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'head': object 'x' not found`

roderickslieker commented 3 years ago

Hi,

Can you run this bit of code? And see whether you have output? This is the input for the colocalization. Are you on CONQUER 1.1.0?

tempfunction <- function(rsID) { cat(rsID,"\n") lead <- load(sprintf("./%s.RData", rsID)) tempdata <- get(lead) rm(list = lead)

LD <- tempdata$topHits
eQTLs <- tempdata$eQTLs
eQTLs <- eQTLs[eQTLs$pValue <= eQTLs$pValueThreshold,]
eQTLs <- eQTLs[!is.na(eQTLs$nes),]

all.gencode <- unique(eQTLs$gencodeId)
lg <- length(all.gencode)

if(lg >= 1){
  data.qtls <- lapply(all.gencode, function(g){
    # Get QTL data
    query <- curl::curl_fetch_memory(sprintf("https://gtexportal.org/rest/v1/association/metasoft?gencodeId=%s&datasetId=gtex_v8", g))
    chars_with_Nan <- rawToChar(query$content)
    chars_with_NA <- gsub("NaN",'"NA"',chars_with_Nan)
    data.qtls.temp <- jsonlite::fromJSON(chars_with_NA)[[1]]
    Position <- reshape2::colsplit(data.qtls.temp[,"variantId"], "_", LETTERS[1:5])[,2]
    data.qtls.temp <- data.qtls.temp[which(Position %in% LD$start),]
    rm(Position)
    rownames(data.qtls.temp) <- NULL
    return(data.qtls.temp)
  })
  names(data.qtls) <- all.gencode
  return(data.qtls)
}

}

x <- tempfunction("rs635634") head(x)

Shabs86 commented 3 years ago

I am on the 1.1.0 version packageVersion('CONQUER') [1] ‘1.1.0’

Shabs86 commented 3 years ago

I ran the tempfunction() as you suggested above and I do get the output across all tissues as seen below.

x <- tempfunction("rs635634") rs635634

head(x) $ENSG00000175164.13 Adipose_Subcutaneous.mValue Adipose_Subcutaneous.nes Adipose_Subcutaneous.pValue Adipose_Subcutaneous.se 1 1 -0.53 0.0000000000000000000000000073 0.046 2 1 -0.52 0.0000000000000000000000081673 0.049 3 1 0.53 0.0000000000000000000000117522 0.050 4 1 -0.52 0.0000000000000000000000000127 0.046 5 1 -0.52 0.0000000000000000000000038852 0.049 Adipose_Visceral_Omentum.mValue Adipose_Visceral_Omentum.nes Adipose_Visceral_Omentum.pValue Adipose_Visceral_Omentum.se 1 1 -0.56 0.00000000000000000000000000075 0.048 2 1 -0.55 0.00000000000000000000000344152 0.051 3 1 0.56 0.00000000000000000000003006190 0.053 4 1 -0.55 0.00000000000000000000000002071 0.048 5 1 -0.56 0.00000000000000000000000018339 0.050 Adrenal_Gland.mValue Adrenal_Gland.nes Adrenal_Gland.pValue Adrenal_Gland.se Artery_Aorta.mValue Artery_Aorta.nes 1 1 -0.55 0.000000000186 0.081 0.96 -0.19 2 1 -0.58 0.000000000094 0.085 0.95 -0.18 3 1 0.57 0.000000000603 0.088 0.75 0.16 4 1 -0.55 0.000000000186 0.081 0.88 -0.18 5 1 -0.58 0.000000000094 0.085 0.97 -0.19 Artery_Aorta.pValue Artery_Aorta.se Artery_Coronary.mValue Artery_Coronary.nes Artery_Coronary.pValue Artery_Coronary.se 1 0.00027 0.051 1 -0.26 0.00000087 0.050 2 0.00104 0.055 1 -0.29 0.00000012 0.053 3 0.00378 0.056 1 0.30 0.00000020 0.055 4 0.00038 0.051 1 -0.26 0.00000074 0.050 5 0.00067 0.055 1 -0.29 0.00000015 0.053 Artery_Tibial.mValue Artery_Tibial.nes Artery_Tibial.pValue Artery_Tibial.se Brain_Amygdala.mValue Brain_Amygdala.nes 1 1 -0.28 0.000000000000000018 0.032 0.017 0.066 2 1 -0.29 0.000000000000000767 0.034 0.018 0.004 3 1 0.28 0.000000000000072366 0.036 0.006 -0.023 4 1 -0.29 0.000000000000000012 0.032 0.000 0.066 5 1 -0.28 0.000000000000001020 0.034 0.012 0.004 Brain_Amygdala.pValue Brain_Amygdala.se Brain_Anterior_cingulate_cortex_BA24.mValue 1 0.53 0.10 0.43 2 0.97 0.11 0.54 3 0.83 0.11 0.47 4 0.53 0.10 0.29 5 0.97 0.11 0.53 Brain_Anterior_cingulate_cortex_BA24.nes Brain_Anterior_cingulate_cortex_BA24.pValue 1 -0.096 0.41 2 -0.115 0.34 3 0.111 0.36 4 -0.096 0.41 5 -0.115 0.34 Brain_Anterior_cingulate_cortex_BA24.se Brain_Caudate_basal_ganglia.mValue Brain_Caudate_basal_ganglia.nes 1 0.12 0.53 -0.16 2 0.12 0.80 -0.17 3 0.12 0.83 0.17 4 0.12 0.55 -0.16 5 0.12 0.75 -0.17 Brain_Caudate_basal_ganglia.pValue Brain_Caudate_basal_ganglia.se Brain_Cerebellar_Hemisphere.mValue 1 0.039 0.075 0.97 2 0.026 0.077 0.93 3 0.030 0.079 0.94 4 0.030 0.075 0.94 5 0.034 0.078 0.92 Brain_Cerebellar_Hemisphere.nes Brain_Cerebellar_Hemisphere.pValue Brain_Cerebellar_Hemisphere.se Brain_Cerebellum.mValue 1 -0.25 0.016 0.1 1.00 2 -0.22 0.030 0.1 1.00 3 0.21 0.049 0.1 0.98 4 -0.25 0.016 0.1 1.00 5 -0.22 0.030 0.1 0.98 Brain_Cerebellum.nes Brain_Cerebellum.pValue Brain_Cerebellum.se Brain_Cortex.mValue Brain_Cortex.nes Brain_Cortex.pValue 1 -0.30 0.00012 0.077 0.28 -0.13 0.17 2 -0.27 0.00099 0.080 0.31 -0.10 0.28 3 0.23 0.00484 0.082 0.34 0.12 0.22 4 -0.30 0.00012 0.077 0.32 -0.13 0.17 5 -0.27 0.00099 0.080 0.22 -0.10 0.28 Brain_Cortex.se Brain_Frontal_Cortex_BA9.mValue Brain_Frontal_Cortex_BA9.nes Brain_Frontal_Cortex_BA9.pValue 1 0.092 0.66 -0.16 0.12 2 0.095 0.78 -0.16 0.13 3 0.098 0.91 0.18 0.11 4 0.092 0.63 -0.16 0.12 5 0.095 0.68 -0.16 0.13 Brain_Frontal_Cortex_BA9.se Brain_Hippocampus.mValue Brain_Hippocampus.nes Brain_Hippocampus.pValue Brain_Hippocampus.se 1 0.10 0.77 -0.18 0.025 0.079 2 0.11 0.24 -0.12 0.136 0.081 3 0.11 0.64 0.14 0.084 0.083 4 0.10 0.87 -0.18 0.025 0.079 5 0.11 0.26 -0.12 0.136 0.081 Brain_Hypothalamus.mValue Brain_Hypothalamus.nes Brain_Hypothalamus.pValue Brain_Hypothalamus.se 1 0.99 -0.27 0.0029 0.088 2 1.00 -0.28 0.0018 0.089 3 0.99 0.28 0.0029 0.092 4 1.00 -0.27 0.0029 0.088 5 0.99 -0.28 0.0018 0.089 Brain_Nucleus_accumbens_basal_ganglia.mValue Brain_Nucleus_accumbens_basal_ganglia.nes 1 1 -0.28 2 1 -0.27 3 1 0.27 4 1 -0.28 5 1 -0.27 Brain_Nucleus_accumbens_basal_ganglia.pValue Brain_Nucleus_accumbens_basal_ganglia.se Brain_Putamen_basal_ganglia.mValue 1 0.00011 0.069 0.89 2 0.00024 0.070 0.70 3 0.00028 0.072 0.58 4 0.00011 0.069 0.82 5 0.00024 0.070 0.59 Brain_Putamen_basal_ganglia.nes Brain_Putamen_basal_ganglia.pValue Brain_Putamen_basal_ganglia.se 1 -0.18 0.006 0.065 2 -0.16 0.017 0.066 3 0.16 0.017 0.067 4 -0.18 0.006 0.065 5 -0.16 0.017 0.066 Brain_Spinal_cord_cervical_c-1.mValue Brain_Spinal_cord_cervical_c-1.nes Brain_Spinal_cord_cervical_c-1.pValue 1 1 -0.34 0.00029 2 1 -0.32 0.00112 3 1 0.34 0.00059 4 1 -0.34 0.00029 5 1 -0.32 0.00112 Brain_Spinal_cord_cervical_c-1.se Brain_Substantia_nigra.mValue Brain_Substantia_nigra.nes Brain_Substantia_nigra.pValue 1 0.091 1 -0.38 0.00052 2 0.094 1 -0.33 0.00376 3 0.095 1 0.31 0.00846 4 0.091 1 -0.38 0.00052 5 0.094 1 -0.33 0.00376 Brain_Substantia_nigra.se Breast_Mammary_Tissue.mValue Breast_Mammary_Tissue.nes Breast_Mammary_Tissue.pValue 1 0.10 1 -0.43 0.000000000146 2 0.11 1 -0.44 0.000000000658 3 0.11 1 0.49 0.000000000027 4 0.10 1 -0.43 0.000000000224 5 0.11 1 -0.45 0.000000000507 Breast_Mammary_Tissue.se Cells_Cultured_fibroblasts.mValue Cells_Cultured_fibroblasts.nes Cells_Cultured_fibroblasts.pValue 1 0.065 NA NA NA 2 0.070 NA NA NA 3 0.070 NA NA NA 4 0.065 NA NA NA 5 0.070 NA NA NA Cells_Cultured_fibroblasts.se Cells_EBV-transformed_lymphocytes.mValue Cells_EBV-transformed_lymphocytes.nes 1 NA 0.000 0.27 2 NA 0.000 0.35 3 NA 0.000 -0.39 4 NA 0.000 0.27 5 NA 0.016 0.35 Cells_EBV-transformed_lymphocytes.pValue Cells_EBV-transformed_lymphocytes.se Colon_Sigmoid.mValue Colon_Sigmoid.nes 1 0.0312 0.12 1 -0.28 2 0.0093 0.13 1 -0.29 3 0.0043 0.14 1 0.28 4 0.0312 0.12 1 -0.27 5 0.0093 0.13 1 -0.29 Colon_Sigmoid.pValue Colon_Sigmoid.se Colon_Transverse.mValue Colon_Transverse.nes Colon_Transverse.pValue 1 0.0000000091 0.047 0.000 -0.13 0.000032 2 0.0000000076 0.048 0.000 -0.14 0.000024 3 0.0000000469 0.050 0.000 0.13 0.000091 4 0.0000000122 0.047 0.000 -0.13 0.000037 5 0.0000000057 0.048 0.002 -0.14 0.000021 Colon_Transverse.se Esophagus_Gastroesophageal_Junction.mValue Esophagus_Gastroesophageal_Junction.nes 1 0.030 1 -0.31 2 0.032 1 -0.30 3 0.033 1 0.31 4 0.030 1 -0.31 5 0.032 1 -0.30 Esophagus_Gastroesophageal_Junction.pValue Esophagus_Gastroesophageal_Junction.se Esophagus_Mucosa.mValue 1 0.00000022 0.058 1 2 0.00000169 0.062 1 3 0.00000191 0.064 1 4 0.00000022 0.058 1 5 0.00000169 0.062 1 Esophagus_Mucosa.nes Esophagus_Mucosa.pValue Esophagus_Mucosa.se Esophagus_Muscularis.mValue Esophagus_Muscularis.nes 1 -0.36 0.0000000000015 0.050 1 -0.41 2 -0.36 0.0000000000123 0.052 1 -0.40 3 0.36 0.0000000000236 0.053 1 0.42 4 -0.36 0.0000000000032 0.050 1 -0.41 5 -0.37 0.0000000000059 0.052 1 -0.41 Esophagus_Muscularis.pValue Esophagus_Muscularis.se Heart_Atrial_Appendage.mValue Heart_Atrial_Appendage.nes 1 0.000000000000017 0.052 1 -0.43 2 0.000000000001781 0.055 1 -0.37 3 0.000000000000484 0.056 1 0.39 4 0.000000000000036 0.052 1 -0.43 5 0.000000000000835 0.055 1 -0.38 Heart_Atrial_Appendage.pValue Heart_Atrial_Appendage.se Heart_Left_Ventricle.mValue Heart_Left_Ventricle.nes 1 0.0000000000058 0.060 1 -0.41 2 0.0000000245268 0.065 1 -0.38 3 0.0000000148681 0.066 1 0.37 4 0.0000000000138 0.061 1 -0.40 5 0.0000000081062 0.065 1 -0.38 Heart_Left_Ventricle.pValue Heart_Left_Ventricle.se Kidney_Cortex.mValue Kidney_Cortex.nes Kidney_Cortex.pValue 1 0.0000000000000000045 0.044 1.00 -0.47 0.00206 2 0.0000000000001097510 0.049 1.00 -0.53 0.00092 3 0.0000000000010159800 0.050 0.98 0.53 0.00092 4 0.0000000000000000098 0.044 0.99 -0.47 0.00206 5 0.0000000000000557248 0.049 0.98 -0.53 0.00092 Kidney_Cortex.se Liver.mValue Liver.nes Liver.pValue Liver.se Lung.mValue Lung.nes Lung.pValue Lung.se 1 0.14 1 -0.67 0.00000000026 0.099 0.96 -0.18 0.00000717 0.040 2 0.15 1 -0.68 0.00000000357 0.109 1.00 -0.20 0.00000365 0.042 3 0.15 1 0.66 0.00000001288 0.111 1.00 0.21 0.00000094 0.043 4 0.14 1 -0.66 0.00000000055 0.100 0.97 -0.19 0.00000523 0.040 5 0.15 1 -0.68 0.00000000258 0.108 1.00 -0.19 0.00000515 0.042 Minor_Salivary_Gland.mValue Minor_Salivary_Gland.nes Minor_Salivary_Gland.pValue Minor_Salivary_Gland.se 1 0.21 -0.049 0.69 0.12 2 0.88 -0.200 0.11 0.12 3 0.77 0.194 0.13 0.13 4 0.11 -0.049 0.69 0.12 5 0.87 -0.200 0.11 0.12 Muscle_Skeletal.mValue Muscle_Skeletal.nes Muscle_Skeletal.pValue Muscle_Skeletal.se Nerve_Tibial.mValue 1 1 -0.50 0.00000000000000000000006 0.049 1 2 1 -0.46 0.00000000000000000915814 0.052 1 3 1 0.46 0.00000000000000010268300 0.054 1 4 1 -0.50 0.00000000000000000000022 0.049 1 5 1 -0.47 0.00000000000000000228858 0.052 1 Nerve_Tibial.nes Nerve_Tibial.pValue Nerve_Tibial.se Ovary.mValue Ovary.nes Ovary.pValue Ovary.se Pancreas.mValue 1 -0.29 0.000000055 0.052 0.99 -0.24 0.0027 0.080 1 2 -0.29 0.000000075 0.053 1.00 -0.24 0.0061 0.085 1 3 0.30 0.000000078 0.054 0.92 0.21 0.0201 0.088 1 4 -0.28 0.000000090 0.052 0.98 -0.24 0.0027 0.080 1 5 -0.29 0.000000066 0.053 1.00 -0.24 0.0061 0.085 1 Pancreas.nes Pancreas.pValue Pancreas.se Pituitary.mValue Pituitary.nes Pituitary.pValue Pituitary.se Prostate.mValue 1 -0.36 0.00016 0.093 1 -0.42 0.0000000000082 0.058 0 2 -0.36 0.00035 0.098 1 -0.40 0.0000000004336 0.061 0 3 0.34 0.00118 0.103 1 0.40 0.0000000009463 0.062 0 4 -0.36 0.00016 0.093 1 -0.42 0.0000000000082 0.058 0 5 -0.36 0.00035 0.098 1 -0.40 0.0000000004336 0.061 0 Prostate.nes Prostate.pValue Prostate.se Skin_Not_Sun_Exposed_Suprapubic.mValue Skin_Not_Sun_Exposed_Suprapubic.nes 1 0.018 0.81 0.072 0.87 -0.19 2 -0.025 0.74 0.075 0.79 -0.17 3 0.034 0.66 0.077 0.75 0.17 4 0.018 0.81 0.072 0.88 -0.18 5 -0.025 0.74 0.075 0.83 -0.18 Skin_Not_Sun_Exposed_Suprapubic.pValue Skin_Not_Sun_Exposed_Suprapubic.se Skin_Sun_Exposed_Lower_leg.mValue 1 0.0051 0.067 0.048 2 0.0167 0.071 0.101 3 0.0220 0.072 0.012 4 0.0068 0.067 0.000 5 0.0132 0.071 0.111 Skin_Sun_Exposed_Lower_leg.nes Skin_Sun_Exposed_Lower_leg.pValue Skin_Sun_Exposed_Lower_leg.se 1 -0.108 0.079 0.061 2 -0.120 0.063 0.064 3 0.095 0.151 0.066 4 -0.099 0.107 0.061 5 -0.129 0.045 0.064 Small_Intestine_Terminal_Ileum.mValue Small_Intestine_Terminal_Ileum.nes Small_Intestine_Terminal_Ileum.pValue 1 0 -0.0086 0.85 2 0 -0.0292 0.53 3 0 0.0499 0.29 4 0 -0.0086 0.85 5 0 -0.0292 0.53 Small_Intestine_Terminal_Ileum.se Spleen.mValue Spleen.nes Spleen.pValue Spleen.se Stomach.mValue Stomach.nes 1 0.045 1 -0.53 0.000000017 0.090 0.000 -0.057 2 0.046 1 -0.56 0.000000068 0.099 0.000 -0.074 3 0.047 1 0.55 0.000000365 0.104 0.000 0.075 4 0.045 1 -0.53 0.000000021 0.090 0.000 -0.058 5 0.046 1 -0.56 0.000000058 0.098 0.006 -0.073 Stomach.pValue Stomach.se Testis.mValue Testis.nes Testis.pValue Testis.se Thyroid.mValue Thyroid.nes Thyroid.pValue 1 0.29 0.053 0.63 -0.16 0.001601 0.052 0.000 -0.086 0.084 2 0.20 0.057 1.00 -0.21 0.000058 0.052 0.000 -0.077 0.141 3 0.20 0.058 1.00 0.22 0.000081 0.054 0.000 0.047 0.377 4 0.28 0.054 0.45 -0.16 0.001881 0.052 0.000 -0.087 0.081 5 0.20 0.057 1.00 -0.22 0.000047 0.052 0.005 -0.075 0.151 Thyroid.se Uterus.mValue Uterus.nes Uterus.pValue Uterus.se Vagina.mValue Vagina.nes Vagina.pValue Vagina.se 1 0.050 1.00 -0.40 0.0020 0.12 1 -0.41 0.000020 0.092 2 0.052 1.00 -0.38 0.0047 0.13 1 -0.42 0.000042 0.099 3 0.053 1.00 0.39 0.0041 0.13 1 0.43 0.000043 0.102 4 0.050 1.00 -0.40 0.0020 0.12 1 -0.41 0.000020 0.092 5 0.052 1.00 -0.38 0.0047 0.13 1 -0.42 0.000042 0.099 Whole_Blood.mValue Whole_Blood.nes Whole_Blood.pValue Whole_Blood.se datasetId gencodeId 1 0 0.69 0.00000000000000000000000000000164160 0.057 gtex_v8 ENSG00000175164.13 2 0 0.76 0.00000000000000000000000000000000036 0.059 gtex_v8 ENSG00000175164.13 3 0 -0.74 0.00000000000000000000000000000172723 0.061 gtex_v8 ENSG00000175164.13 4 0 0.70 0.00000000000000000000000000000018430 0.057 gtex_v8 ENSG00000175164.13 5 0 0.75 0.00000000000000000000000000000000391 0.059 gtex_v8 ENSG00000175164.13 metaP 1 0.000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000052 2 0.000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001232459999999999377307165204786799 3 0.000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000893568999999999395104227639663463378383312374353 4 0.000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000969155 5 0.000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000331260999999999874391504173232 variantId 1 chr9_133276354_C_T_b38 2 chr9_133279427_T_C_b38 3 chr9_133274295_A_T_b38 4 chr9_133278431_T_C_b38 5 chr9_133274414_A_G_b38 [ reached getOption("max.print") -- omitted 2 rows ]

$ENSG00000148290.9 Adipose_Subcutaneous.mValue Adipose_Subcutaneous.nes Adipose_Subcutaneous.pValue Adipose_Subcutaneous.se 1 1 0.27 0.000000000244 0.042 2 1 0.25 0.000000001554 0.041 3 1 0.25 0.000000001867 0.041 4 1 0.25 0.000000001403 0.041 5 1 0.27 0.000000000216 0.042 Adipose_Visceral_Omentum.mValue Adipose_Visceral_Omentum.nes Adipose_Visceral_Omentum.pValue Adipose_Visceral_Omentum.se 1 1 0.24 0.0000000012407 0.039 2 1 0.22 0.0000000165035 0.038 3 1 0.22 0.0000000221694 0.038 4 1 0.21 0.0000000369536 0.038 5 1 0.24 0.0000000017122 0.039 Adrenal_Gland.mValue Adrenal_Gland.nes Adrenal_Gland.pValue Adrenal_Gland.se Artery_Aorta.mValue Artery_Aorta.nes 1 0.97 0.18 0.040 0.085 1.00 0.19 2 1.00 0.21 0.011 0.080 0.99 0.17 3 0.99 0.21 0.011 0.080 0.95 0.17 4 1.00 0.21 0.011 0.080 1.00 0.16 5 1.00 0.18 0.040 0.085 1.00 0.19 Artery_Aorta.pValue Artery_Aorta.se Artery_Coronary.mValue Artery_Coronary.nes Artery_Coronary.pValue Artery_Coronary.se 1 0.000400 0.054 0.92 0.13 0.048 0.068 2 0.000788 0.050 0.99 0.14 0.024 0.063 3 0.001105 0.050 1.00 0.14 0.031 0.064 4 0.001280 0.050 0.99 0.14 0.031 0.064 5 0.000584 0.054 0.94 0.13 0.061 0.068 Artery_Tibial.mValue Artery_Tibial.nes Artery_Tibial.pValue Artery_Tibial.se Brain_Amygdala.mValue Brain_Amygdala.nes 1 1 0.18 0.000000558 0.036 1 0.35 2 1 0.20 0.000000015 0.034 1 0.33 3 1 0.19 0.000000034 0.034 1 0.33 4 1 0.19 0.000000039 0.034 1 0.33 5 1 0.18 0.000001080 0.036 1 0.35 Brain_Amygdala.pValue Brain_Amygdala.se Brain_Anterior_cingulate_cortex_BA24.mValue 1 0.00067 0.101 1 2 0.00108 0.098 1 3 0.00108 0.098 1 4 0.00108 0.098 1 5 0.00067 0.101 1 Brain_Anterior_cingulate_cortex_BA24.nes Brain_Anterior_cingulate_cortex_BA24.pValue 1 0.39 0.000034 2 0.36 0.000080 3 0.36 0.000080 4 0.36 0.000080 5 0.39 0.000034 Brain_Anterior_cingulate_cortex_BA24.se Brain_Caudate_basal_ganglia.mValue Brain_Caudate_basal_ganglia.nes 1 0.090 1 0.36 2 0.087 1 0.36 3 0.087 1 0.35 4 0.087 1 0.35 5 0.090 1 0.35 Brain_Caudate_basal_ganglia.pValue 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Brain_Hippocampus.mValue Brain_Hippocampus.nes Brain_Hippocampus.pValue Brain_Hippocampus.se 1 0.096 1 0.31 0.00087 0.092 2 0.092 1 0.34 0.00026 0.089 3 0.092 1 0.34 0.00026 0.089 4 0.092 1 0.34 0.00026 0.089 5 0.096 1 0.31 0.00087 0.092 Brain_Hypothalamus.mValue Brain_Hypothalamus.nes Brain_Hypothalamus.pValue Brain_Hypothalamus.se 1 1 0.32 0.000084 0.080 2 1 0.33 0.000040 0.079 3 1 0.33 0.000040 0.079 4 1 0.33 0.000040 0.079 5 1 0.32 0.000084 0.080 Brain_Nucleus_accumbens_basal_ganglia.mValue Brain_Nucleus_accumbens_basal_ganglia.nes 1 1 0.35 2 1 0.34 3 1 0.34 4 1 0.34 5 1 0.35 Brain_Nucleus_accumbens_basal_ganglia.pValue Brain_Nucleus_accumbens_basal_ganglia.se Brain_Putamen_basal_ganglia.mValue 1 0.000082 0.086 1 2 0.000097 0.085 1 3 0.000097 0.085 1 4 0.000097 0.085 1 5 0.000082 0.086 1 Brain_Putamen_basal_ganglia.nes Brain_Putamen_basal_ganglia.pValue Brain_Putamen_basal_ganglia.se 1 0.45 0.0000118 0.099 2 0.44 0.0000237 0.099 3 0.44 0.0000237 0.099 4 0.44 0.0000237 0.099 5 0.45 0.0000118 0.099 Brain_Spinal_cord_cervical_c-1.mValue Brain_Spinal_cord_cervical_c-1.nes Brain_Spinal_cord_cervical_c-1.pValue 1 1.00 0.44 0.000078 2 0.98 0.37 0.000712 3 1.00 0.37 0.000712 4 1.00 0.37 0.000712 5 1.00 0.44 0.000078 Brain_Spinal_cord_cervical_c-1.se Brain_Substantia_nigra.mValue Brain_Substantia_nigra.nes Brain_Substantia_nigra.pValue 1 0.11 1.00 0.39 0.00088 2 0.11 1.00 0.37 0.00105 3 0.11 1.00 0.37 0.00105 4 0.11 1.00 0.37 0.00105 5 0.11 0.99 0.39 0.00088 Brain_Substantia_nigra.se Breast_Mammary_Tissue.mValue Breast_Mammary_Tissue.nes Breast_Mammary_Tissue.pValue 1 0.11 1 0.23 0.000000380 2 0.11 1 0.20 0.000002016 3 0.11 1 0.21 0.000001458 4 0.11 1 0.20 0.000001623 5 0.11 1 0.23 0.000000254 Breast_Mammary_Tissue.se Cells_Cultured_fibroblasts.mValue Cells_Cultured_fibroblasts.nes Cells_Cultured_fibroblasts.pValue 1 0.044 1 0.22 0.0000856 2 0.042 1 0.23 0.0000105 3 0.042 1 0.23 0.0000079 4 0.042 1 0.23 0.0000094 5 0.044 1 0.22 0.0000768 Cells_Cultured_fibroblasts.se Cells_EBV-transformed_lymphocytes.mValue Cells_EBV-transformed_lymphocytes.nes 1 0.055 1.00 0.25 2 0.052 1.00 0.21 3 0.052 1.00 0.20 4 0.052 0.97 0.21 5 0.055 1.00 0.25 Cells_EBV-transformed_lymphocytes.pValue Cells_EBV-transformed_lymphocytes.se Colon_Sigmoid.mValue Colon_Sigmoid.nes 1 0.0249 0.11 1 0.21 2 0.0456 0.10 1 0.20 3 0.0534 0.10 1 0.19 4 0.0456 0.10 1 0.19 5 0.0249 0.11 1 0.21 Colon_Sigmoid.pValue Colon_Sigmoid.se Colon_Transverse.mValue Colon_Transverse.nes Colon_Transverse.pValue 1 0.0001288 0.054 1 0.35 0.00000000053279 2 0.0001954 0.052 1 0.32 0.00000000078805 3 0.0002842 0.052 1 0.32 0.00000000177896 4 0.0002842 0.052 1 0.32 0.00000000177896 5 0.0001895 0.054 1 0.34 0.00000000123473 Colon_Transverse.se Esophagus_Gastroesophageal_Junction.mValue Esophagus_Gastroesophageal_Junction.nes 1 0.054 1 0.35 2 0.051 1 0.29 3 0.051 1 0.29 4 0.051 1 0.29 5 0.054 1 0.35 Esophagus_Gastroesophageal_Junction.pValue Esophagus_Gastroesophageal_Junction.se Esophagus_Mucosa.mValue 1 0.000000000174 0.052 1 2 0.000000027068 0.050 1 3 0.000000027068 0.050 1 4 0.000000027068 0.050 1 5 0.000000000174 0.052 1 Esophagus_Mucosa.nes Esophagus_Mucosa.pValue Esophagus_Mucosa.se Esophagus_Muscularis.mValue Esophagus_Muscularis.nes 1 0.26 0.00000084 0.052 1 0.30 2 0.26 0.00000031 0.049 1 0.27 3 0.25 0.00000043 0.049 1 0.28 4 0.25 0.00000042 0.049 1 0.28 5 0.26 0.00000114 0.052 1 0.31 Esophagus_Muscularis.pValue Esophagus_Muscularis.se Heart_Atrial_Appendage.mValue Heart_Atrial_Appendage.nes 1 0.0000000124 0.052 1 0.38 2 0.0000000713 0.049 1 0.32 3 0.0000000437 0.049 1 0.32 4 0.0000000437 0.049 1 0.31 5 0.0000000072 0.052 1 0.37 Heart_Atrial_Appendage.pValue Heart_Atrial_Appendage.se Heart_Left_Ventricle.mValue Heart_Left_Ventricle.nes 1 0.00000000000195 0.051 1 0.32 2 0.00000000062624 0.050 1 0.29 3 0.00000000075134 0.050 1 0.28 4 0.00000000134995 0.050 1 0.28 5 0.00000000000221 0.051 1 0.31 Heart_Left_Ventricle.pValue Heart_Left_Ventricle.se Kidney_Cortex.mValue 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0.00000000066 0.039 1 0.19 3 1 0.24 0.00000000186 0.039 1 0.19 4 1 0.24 0.00000000131 0.039 1 0.19 5 1 0.24 0.00000001614 0.041 1 0.21 Nerve_Tibial.pValue Nerve_Tibial.se Ovary.mValue Ovary.nes Ovary.pValue Ovary.se Pancreas.mValue Pancreas.nes 1 0.000000364 0.041 0.89 0.119 0.14 0.081 1 0.16 2 0.000002055 0.040 0.83 0.090 0.24 0.077 1 0.16 3 0.000003633 0.040 0.92 0.098 0.21 0.077 1 0.16 4 0.000002876 0.040 0.88 0.090 0.24 0.077 1 0.16 5 0.000000672 0.041 0.92 0.119 0.14 0.081 1 0.16 Pancreas.pValue Pancreas.se Pituitary.mValue Pituitary.nes Pituitary.pValue Pituitary.se Prostate.mValue Prostate.nes 1 0.001258 0.051 1 0.26 0.00057 0.074 1 0.24 2 0.000897 0.048 1 0.24 0.00080 0.071 1 0.21 3 0.000897 0.048 1 0.24 0.00110 0.071 1 0.21 4 0.000897 0.048 1 0.24 0.00080 0.071 1 0.21 5 0.001258 0.051 1 0.26 0.00057 0.074 1 0.24 Prostate.pValue Prostate.se Skin_Not_Sun_Exposed_Suprapubic.mValue Skin_Not_Sun_Exposed_Suprapubic.nes 1 0.000162 0.062 1 0.24 2 0.000491 0.060 1 0.24 3 0.000491 0.060 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0.019 gtex_v8 ENSG00000148290.9 4 0 0.074 0.0001651 0.019 gtex_v8 ENSG00000148290.9 5 0 0.087 0.0000213 0.020 gtex_v8 ENSG00000148290.9 metaP 1 0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000081929099999999975851433520190881 2 0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000056890999999999975651754358096923169796355 3 0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000416134999999999805834344224209075946419034153 4 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$ENSG00000148300.11 Adipose_Subcutaneous.mValue Adipose_Subcutaneous.nes Adipose_Subcutaneous.pValue Adipose_Subcutaneous.se 1 0.15 -0.031 0.30 0.03 2 0.30 -0.034 0.25 0.03 Adipose_Visceral_Omentum.mValue Adipose_Visceral_Omentum.nes Adipose_Visceral_Omentum.pValue Adipose_Visceral_Omentum.se 1 0.17 -0.024 0.42 0.029 2 0.28 -0.028 0.35 0.029 Adrenal_Gland.mValue Adrenal_Gland.nes Adrenal_Gland.pValue Adrenal_Gland.se Artery_Aorta.mValue Artery_Aorta.nes 1 0.19 0.0067 0.92 0.067 0.14 -0.012 2 0.26 0.0067 0.92 0.067 0.26 -0.012 Artery_Aorta.pValue Artery_Aorta.se Artery_Coronary.mValue Artery_Coronary.nes Artery_Coronary.pValue Artery_Coronary.se 1 0.73 0.035 0.2 0.047 0.42 0.059 2 0.73 0.035 0.3 0.050 0.40 0.059 Artery_Tibial.mValue Artery_Tibial.nes Artery_Tibial.pValue Artery_Tibial.se Brain_Amygdala.mValue Brain_Amygdala.nes 1 0.21 -0.076 0.015 0.031 0.21 -0.027 2 0.31 -0.077 0.014 0.031 0.26 -0.027 Brain_Amygdala.pValue Brain_Amygdala.se Brain_Anterior_cingulate_cortex_BA24.mValue 1 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Esophagus_Gastroesophageal_Junction.pValue Esophagus_Gastroesophageal_Junction.se Esophagus_Mucosa.mValue 1 0.76 0.041 0.15 2 0.76 0.041 0.25 Esophagus_Mucosa.nes Esophagus_Mucosa.pValue Esophagus_Mucosa.se Esophagus_Muscularis.mValue Esophagus_Muscularis.nes 1 -0.0064 0.84 0.032 0.14 -0.010 2 -0.0066 0.84 0.032 0.27 -0.015 Esophagus_Muscularis.pValue Esophagus_Muscularis.se Heart_Atrial_Appendage.mValue Heart_Atrial_Appendage.nes 1 0.76 0.032 0.15 -0.0032 2 0.65 0.032 0.23 0.0019 Heart_Atrial_Appendage.pValue Heart_Atrial_Appendage.se Heart_Left_Ventricle.mValue Heart_Left_Ventricle.nes 1 0.94 0.041 0.11 0.0091 2 0.96 0.041 0.25 0.0064 Heart_Left_Ventricle.pValue Heart_Left_Ventricle.se Kidney_Cortex.mValue Kidney_Cortex.nes Kidney_Cortex.pValue 1 0.80 0.037 0.20 0.024 0.83 2 0.86 0.037 0.24 0.024 0.83 Kidney_Cortex.se Liver.mValue Liver.nes Liver.pValue Liver.se Lung.mValue Lung.nes Lung.pValue Lung.se 1 0.11 0.22 0.054 0.41 0.065 0.099 0.022 0.40 0.025 2 0.11 0.34 0.062 0.35 0.066 0.265 0.021 0.42 0.025 Minor_Salivary_Gland.mValue Minor_Salivary_Gland.nes Minor_Salivary_Gland.pValue Minor_Salivary_Gland.se 1 0.15 0.077 0.31 0.076 2 0.32 0.077 0.31 0.076 Muscle_Skeletal.mValue Muscle_Skeletal.nes Muscle_Skeletal.pValue Muscle_Skeletal.se Nerve_Tibial.mValue Nerve_Tibial.nes 1 0.19 -0.024 0.23 0.02 0.092 0.012 2 0.33 -0.026 0.20 0.02 0.251 0.011 Nerve_Tibial.pValue Nerve_Tibial.se Ovary.mValue Ovary.nes Ovary.pValue Ovary.se Pancreas.mValue Pancreas.nes 1 0.65 0.027 0.15 0.0074 0.9 0.057 0.20 0.033 2 0.68 0.027 0.27 0.0074 0.9 0.057 0.32 0.033 Pancreas.pValue Pancreas.se Pituitary.mValue Pituitary.nes Pituitary.pValue Pituitary.se Prostate.mValue Prostate.nes 1 0.51 0.05 0.13 0.025 0.69 0.063 0.18 -0.14 2 0.51 0.05 0.32 0.025 0.69 0.063 0.30 -0.14 Prostate.pValue Prostate.se Skin_Not_Sun_Exposed_Suprapubic.mValue Skin_Not_Sun_Exposed_Suprapubic.nes 1 0.04 0.065 0.18 -0.030 2 0.04 0.065 0.28 -0.027 Skin_Not_Sun_Exposed_Suprapubic.pValue Skin_Not_Sun_Exposed_Suprapubic.se Skin_Sun_Exposed_Lower_leg.mValue 1 0.29 0.028 0.18 2 0.34 0.028 0.32 Skin_Sun_Exposed_Lower_leg.nes Skin_Sun_Exposed_Lower_leg.pValue Skin_Sun_Exposed_Lower_leg.se 1 -0.023 0.31 0.023 2 -0.025 0.27 0.023 Small_Intestine_Terminal_Ileum.mValue Small_Intestine_Terminal_Ileum.nes Small_Intestine_Terminal_Ileum.pValue 1 0.17 -0.044 0.49 2 0.28 -0.044 0.49 Small_Intestine_Terminal_Ileum.se Spleen.mValue Spleen.nes Spleen.pValue Spleen.se Stomach.mValue Stomach.nes 1 0.064 0.17 0.017 0.77 0.056 0.15 0.062 2 0.064 0.26 0.023 0.69 0.056 0.26 0.064 Stomach.pValue Stomach.se Testis.mValue Testis.nes Testis.pValue Testis.se Thyroid.mValue Thyroid.nes Thyroid.pValue 1 0.17 0.045 0.18 -0.089 0.101 0.054 0.15 -0.019 0.45 2 0.16 0.045 0.27 -0.092 0.092 0.054 0.30 -0.025 0.32 Thyroid.se Uterus.mValue Uterus.nes Uterus.pValue Uterus.se Vagina.mValue Vagina.nes Vagina.pValue Vagina.se 1 0.025 0.16 -0.01 0.91 0.091 0.15 0.06 0.49 0.086 2 0.025 0.25 -0.01 0.91 0.091 0.26 0.06 0.49 0.086 Whole_Blood.mValue Whole_Blood.nes Whole_Blood.pValue Whole_Blood.se datasetId gencodeId metaP 1 0.14 0.022 0.38 0.025 gtex_v8 ENSG00000148300.11 0.115 2 0.21 0.022 0.36 0.025 gtex_v8 ENSG00000148300.11 0.082 variantId 1 chr9_133274414_A_G_b38 2 chr9_133279427_T_C_b38

roderickslieker commented 3 years ago

You have the coloc package installed right? Your connection to GTEx API is fine. What you could check now is using your created object x:

load("rs635634.RData") LD <- rs635634$topHits

allColoc <- lapply(names(x), CONQUER:::calculateColocalization, data.qtls=x, LD=LD) %>% do.call(what=rbind)

If that doesn't work you can check which gene is failing by looking at the names of x, there should be three genes, and run them one by one to see where there is an error.

Shabs86 commented 3 years ago

Only for rs635634 I get the allColoc output. For the rest of rsids I get NULL.

roderickslieker commented 3 years ago

OK so that's making stuff even weirder. If you do it manually it works, but within the package environment it doesn't work. Did you set your working directory to the directory of the SNP file and loaded the coloc package (just to be sure)?

Shabs86 commented 3 years ago

So, I have tried this on a different system (mac) and the problem still exists. Could it be these particular snp related issue? Could you please share what outputs you get when you run the same initial command with the snps I used? Also, is there a way to fasten the process when running a bunch of snps? As of now, it takes a few days to finish for around 100 ish snps.

Regarding the installation procedure, I used the standalone zip for conquer (>1.5G) as the normal way of downloading over the internet wasn't stable. Could that be an issue?

Shabs86 commented 3 years ago

And yeah, I even tried after loading all the installed R packages and still the same result.

roderickslieker commented 3 years ago

Hm CONQUER.db hasn't been updated much. So that can't be it. Can you try to update CONQUER using devtools::install_github("roderickslieker/CONQUER"). If you drop me an email (r.c.slieker at lumc.nl) I can sent you the files for the five snps. But it should just work in your hands as well. In terms of speed: it's so slow because we re-calculate the SNPs (cis and some trans ones) on the GTEx API. I am wondering whether we should just add a fast function for those people that want to use the precooked SNPs by GTEx. That should be much faster.

roderickslieker commented 3 years ago

Any news? To improve speed I've now implemented an argument that will take the eQTLs from GTEx as is. This makes the whole process much faster, but not that you may miss eQTLs as GTEx does only test those genes with a TSSS within 1MB of the SNP.

SKVirk27 commented 2 years ago

devtools::install_github("roderickslieker/CONQUER.d3") Error: .onLoad failed in loadNamespace() for 'pkgload', details: call: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) error: namespace ‘rlang’ 1.0.0 is already loaded, but >= 1.0.1 is required

SKVirk27 commented 2 years ago

how I can fix this error.