Get list of predictor SNPs and weights in predictdb
how_to
To get a list of SNPs and the corresponding weights to predict expression levels (or splicing) of a given gene, you will first need to download the databases where the prediction models are stored. For example, you can download them from here more specifically from this tar file
On CRI they are located in /gpfs/data/im-lab/nas40t2/Data/PredictDB/GTEx_v8/models_v1/eqtl/mashr/
Here I will mount the drive to my local machine following these instructions
library(tidyverse)## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
## ✓ ggplot2 3.3.3 ✓ purrr 0.3.4
## ✓ tibble 3.1.2 ✓ dplyr 1.0.6
## ✓ tidyr 1.1.3 ✓ stringr 1.4.0
## ✓ readr 1.4.0 ✓ forcats 0.5.1
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()model_dir = "/Volumes/im-lab/nas40t2/Data/PredictDB/GTEx_v8/models_v1/eqtl/mashr"Get ensemblid for the gene. For example GSDMA’s ensid is ENSG00000167914
## install.packages("RSQLite")
library("RSQLite")
sqlite <- dbDriver("SQLite")
df = data.frame()
dbnamelist= list.files(model_dir,pattern = "*.db")
for(dbname in dbnamelist)
{
print("--")
print(dbname)
## connect to db
db = dbConnect(sqlite,glue::glue("{model_dir}/{dbname}"))
## list tables
tempo <- dbGetQuery(db,"select * from weights where gene like 'ENSG00000167914%'") ## % is wildcard, to avoid dealing with ENSG version number
if(nrow(tempo)>0)
{
tempo$tissue <- gsub("mashr_","",gsub(".db","",dbname))
df = rbind(df,tempo)
}
}## [1] "--"
## [1] "mashr_Adipose_Subcutaneous.db"
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## [1] "mashr_Adipose_Visceral_Omentum.db"
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## [1] "mashr_Adrenal_Gland.db"
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## [1] "mashr_Artery_Aorta.db"
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## [1] "mashr_Artery_Coronary.db"
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## [1] "mashr_Artery_Tibial.db"
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## [1] "mashr_Brain_Amygdala.db"
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## [1] "mashr_Brain_Anterior_cingulate_cortex_BA24.db"
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## [1] "mashr_Brain_Caudate_basal_ganglia.db"
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## [1] "mashr_Brain_Cerebellar_Hemisphere.db"
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## [1] "mashr_Brain_Cerebellum.db"
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## [1] "mashr_Brain_Cortex.db"
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## [1] "mashr_Brain_Frontal_Cortex_BA9.db"
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## [1] "mashr_Brain_Hippocampus.db"
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## [1] "mashr_Brain_Hypothalamus.db"
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## [1] "mashr_Brain_Nucleus_accumbens_basal_ganglia.db"
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## [1] "mashr_Brain_Putamen_basal_ganglia.db"
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## [1] "mashr_Brain_Spinal_cord_cervical_c-1.db"
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## [1] "mashr_Brain_Substantia_nigra.db"
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## [1] "mashr_Breast_Mammary_Tissue.db"
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## [1] "mashr_Cells_Cultured_fibroblasts.db"
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## [1] "mashr_Cells_EBV-transformed_lymphocytes.db"
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## [1] "mashr_Colon_Sigmoid.db"
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## [1] "mashr_Colon_Transverse.db"
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## [1] "mashr_Esophagus_Gastroesophageal_Junction.db"
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## [1] "mashr_Esophagus_Mucosa.db"
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## [1] "mashr_Esophagus_Muscularis.db"
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## [1] "mashr_Heart_Atrial_Appendage.db"
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## [1] "mashr_Heart_Left_Ventricle.db"
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## [1] "mashr_Kidney_Cortex.db"
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## [1] "mashr_Liver.db"
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## [1] "mashr_Lung.db"
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## [1] "mashr_Minor_Salivary_Gland.db"
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## [1] "mashr_Muscle_Skeletal.db"
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## [1] "mashr_Nerve_Tibial.db"
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## [1] "mashr_Ovary.db"
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## [1] "mashr_Pancreas.db"
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## [1] "mashr_Pituitary.db"
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## [1] "mashr_Prostate.db"
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## [1] "mashr_Skin_Not_Sun_Exposed_Suprapubic.db"
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## [1] "mashr_Skin_Sun_Exposed_Lower_leg.db"
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## [1] "mashr_Small_Intestine_Terminal_Ileum.db"
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## [1] "mashr_Spleen.db"
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## [1] "mashr_Stomach.db"
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## [1] "mashr_Testis.db"
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## [1] "mashr_Thyroid.db"
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## [1] "mashr_Uterus.db"
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## [1] "mashr_Vagina.db"
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## [1] "mashr_Whole_Blood.db"df %>% count(rsid,varID) %>% arrange(desc( n))## rsid varID n
## 1 rs3859191 chr17_39972461_G_A_b38 17
## 2 rs28618095 chr17_39952822_T_C_b38 14
## 3 rs4794821 chr17_39967950_T_C_b38 5
## 4 rs4458030 chr17_39965453_G_A_b38 4
## 5 rs4065876 chr17_39973253_G_A_b38 3
## 6 chr17_39954836_G_C_b38 chr17_39954836_G_C_b38 2
## 7 rs3916061 chr17_39971460_A_G_b38 2
## 8 rs56326707 chr17_39973886_C_T_b38 2
## 9 rs59269632 chr17_39969978_A_G_b38 2
## 10 rs60667221 chr17_39954137_T_A_b38 2
## 11 rs921651 chr17_39977669_G_A_b38 2
## 12 rs113277605 chr17_40000142_C_T_b38 1
## 13 rs3859192 chr17_39972395_C_T_b38 1
## 14 rs397713502 chr17_39972331_A_AG_b38 1
## 15 rs398100509 chr17_39966991_AC_A_b38 1
## 16 rs4239225 chr17_39970859_G_A_b38 1
## 17 rs56946324 chr17_39951713_C_A_b38 1
## 18 rs60725845 chr17_39968377_T_G_b38 1
## 19 rs7214085 chr17_40012842_T_C_b38 1
## 20 rs7221814 chr17_39933464_A_G_b38 1
## 21 rs72832971 chr17_39952366_C_T_b38 1
## 22 rs796403983 chr17_39972785_AG_A_b38 1
## 23 rs8077456 chr17_39972512_G_C_b38 1write_csv(df,"~/Downloads/GSDMA-weights.csv")Also checkout how to query sqlite database this post