pqtl(
  query,
  rtype = c("mrres", "simple", "sglmr", "inst", "sense"),
  pvalue = 0.05,
  searchflag = c("traits", "proteins"),
  mode = c("table", "raw")
)

Arguments

query

(Required) A protein coding gene name or a trait name, e.g. "ADAM19" or "Inflammatory bowel disease" which cannot be NULL.

rtype

(Optional) A type of data to be extracted, which can be one of these options:

  1. simple: Basic summary

  2. mrres: MR results (DEFAULT)

  3. sglmr: Single SNP MR results

  4. inst: SNP information

  5. sense: Sensitivity analysis NOTE: mrres is a DEFAULT option.

pvalue

(Optional) A pvalue threshold for MR results with the DEFAULT set to 0.05. NOTE: this threshold applies to any rtype chosen.

searchflag

(Required) A flag to indicate whether you are searching for proteins or traits which cannot be NULL. If query is a protein name, then this flag should be "proteins"; if query is a trait, this flag should be "traits". NOTE: if the wrong flag is chosen for query, there will be no result returned.

mode

If mode = "table", returns a data frame (a tibble as per tidyverse convention). If mode = "raw", returns a raw response from EpiGraphDB API with minimal parsing done by httr.

Value

Data from GET /pqtl/

Examples

# Returns a data frame of MR results, while searching for proteins pqtl(query = "ADAM19", searchflag = "proteins")
#> # A tibble: 16 x 8 #> expID outID outID_mrbase nsnp method beta se pvalue #> <chr> <chr> <chr> <int> <chr> <dbl> <dbl> <dbl> #> 1 ADAM19 Forced expirator… UKB-a:337 1 Wald r… 6.82e-2 8.92e-3 2.10e-14 #> 2 ADAM19 Height 89 1 Wald r… 4.88e-2 1.26e-2 1.08e- 4 #> 3 ADAM19 Non-cancer illne… UKB-a:66 1 Wald r… -1.26e-1 3.28e-2 1.21e- 4 #> 4 ADAM19 Hippocampus volu… 1045 1 Wald r… 6.37e+1 2.00e+1 1.48e- 3 #> 5 ADAM19 Forced vital cap… UKB-a:336 1 Wald r… 2.45e-2 8.46e-3 3.71e- 3 #> 6 ADAM19 Diagnoses - main… UKB-a:582 1 Wald r… -1.57e-1 5.85e-2 7.14e- 3 #> 7 ADAM19 Intracranial vol… 1041 1 Wald r… 1.99e+4 8.17e+3 1.50e- 2 #> 8 ADAM19 Neo-conscientiou… 114 1 Wald r… -7.48e-1 3.12e-1 1.66e- 2 #> 9 ADAM19 Subjective well … 1009 1 Wald r… 2.85e-2 1.22e-2 1.96e- 2 #> 10 ADAM19 Invasive mucinou… 1123 1 Wald r… 3.96e-1 1.73e-1 2.18e- 2 #> 11 ADAM19 HDL cholesterol 299 1 Wald r… -4.19e-2 1.99e-2 3.55e- 2 #> 12 ADAM19 Paget's disease 975 1 Wald r… -5.24e-1 2.49e-1 3.56e- 2 #> 13 ADAM19 Fractured bone s… UKB-a:441 1 Wald r… -1.04e-1 4.99e-2 3.69e- 2 #> 14 ADAM19 Diagnoses - main… UKB-a:559 1 Wald r… -1.77e-1 8.64e-2 4.09e- 2 #> 15 ADAM19 Systolic blood p… UKB-a:360 1 Wald r… -2.11e-2 1.05e-2 4.51e- 2 #> 16 ADAM19 Diagnoses - main… UKB-a:574 1 Wald r… -3.70e-1 1.85e-1 4.58e- 2
# Returns a data frame with SNP information, while searching for traits pqtl( query = "Inflammatory bowel disease", rtype = "inst", searchflag = "traits" )
#> # A tibble: 56 x 13 #> rsID expID outID outID_mrbase ea nea eaf_exp sample_exp sample_out #> <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> #> 1 rs11… IL23R Infl… 294 A G 0.0669 3301 65642 #> 2 rs18… FCGR… Infl… 294 G A 0.533 3301 65642 #> 3 rs49… IL12B Infl… 294 C T 0.678 3301 65642 #> 4 rs11… C1QT… Infl… 294 A G 0.472 3301 65642 #> 5 rs98… TXND… Infl… 294 T G 0.110 3301 65642 #> 6 rs18… IL27 Infl… 294 T G 0.327 3301 65642 #> 7 rs10… IL1R… Infl… 294 G T 0.521 3301 65642 #> 8 rs12… FST Infl… 294 T C 0.44 3394 65642 #> 9 rs46… IGFB… Infl… 294 C T 0.555 6861 65642 #> 10 rs12… KLKB1 Infl… 294 T C 0.448 6861 65642 #> # … with 46 more rows, and 4 more variables: author_exp <chr>, #> # author_out <chr>, trans_cis <chr>, pvalue <dbl>
# Change a pvalue threshold (the default is 0.05) pqtl( query = "Inflammatory bowel disease", rtype = "inst", pvalue = 1.0, searchflag = "traits" )
#> # A tibble: 156 x 13 #> rsID expID outID outID_mrbase ea nea eaf_exp sample_exp sample_out #> <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> #> 1 rs11… IL23R Infl… 294 A G 0.0669 3301 65642 #> 2 rs18… FCGR… Infl… 294 G A 0.533 3301 65642 #> 3 rs49… IL12B Infl… 294 C T 0.678 3301 65642 #> 4 rs11… C1QT… Infl… 294 A G 0.472 3301 65642 #> 5 rs98… TXND… Infl… 294 T G 0.110 3301 65642 #> 6 rs18… IL27 Infl… 294 T G 0.327 3301 65642 #> 7 rs10… IL1R… Infl… 294 G T 0.521 3301 65642 #> 8 rs12… FST Infl… 294 T C 0.44 3394 65642 #> 9 rs46… IGFB… Infl… 294 C T 0.555 6861 65642 #> 10 rs12… KLKB1 Infl… 294 T C 0.448 6861 65642 #> # … with 146 more rows, and 4 more variables: author_exp <chr>, #> # author_out <chr>, trans_cis <chr>, pvalue <dbl>
# Returns raw response if mode="raw" pqtl( query = "ADAM19", searchflag = "proteins", mode = "raw" ) %>% str()
#> List of 2 #> $ metadata:List of 3 #> ..$ query : chr "MATCH (e:Exposure)<-[n:SENS_EXP]-(s)-[m:SENS_OUT]-> (o:Outcome)<-[r:MR]-(e:Exposure) WHERE e.expID = \"ADAM19\""| __truncated__ #> ..$ total_seconds: NULL #> ..$ empty_results: logi FALSE #> $ results :List of 16 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "Forced expiratory volume in 1-second (FEV1)" #> .. ..$ outID_mrbase: chr "UKB-a:337" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num 0.0682 #> .. ..$ se : num 0.00892 #> .. ..$ pvalue : num 2.1e-14 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "Height" #> .. ..$ outID_mrbase: chr "89" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num 0.0488 #> .. ..$ se : num 0.0126 #> .. ..$ pvalue : num 0.000108 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "Non-cancer illness code self-reported: asthma" #> .. ..$ outID_mrbase: chr "UKB-a:66" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num -0.126 #> .. ..$ se : num 0.0328 #> .. ..$ pvalue : num 0.000121 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "Hippocampus volume" #> .. ..$ outID_mrbase: chr "1045" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num 63.7 #> .. ..$ se : num 20 #> .. ..$ pvalue : num 0.00148 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "Forced vital capacity (FVC)" #> .. ..$ outID_mrbase: chr "UKB-a:336" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num 0.0245 #> .. ..$ se : num 0.00846 #> .. ..$ pvalue : num 0.00371 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "Diagnoses - main ICD10: R10 Abdominal and pelvic pain" #> .. ..$ outID_mrbase: chr "UKB-a:582" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num -0.157 #> .. ..$ se : num 0.0585 #> .. ..$ pvalue : num 0.00714 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "Intracranial volume" #> .. ..$ outID_mrbase: chr "1041" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num 19878 #> .. ..$ se : num 8174 #> .. ..$ pvalue : num 0.015 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "Neo-conscientiousness" #> .. ..$ outID_mrbase: chr "114" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num -0.748 #> .. ..$ se : num 0.312 #> .. ..$ pvalue : num 0.0166 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "Subjective well being" #> .. ..$ outID_mrbase: chr "1009" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num 0.0285 #> .. ..$ se : num 0.0122 #> .. ..$ pvalue : num 0.0196 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "Invasive mucinous ovarian cancer" #> .. ..$ outID_mrbase: chr "1123" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num 0.396 #> .. ..$ se : num 0.173 #> .. ..$ pvalue : num 0.0218 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "HDL cholesterol" #> .. ..$ outID_mrbase: chr "299" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num -0.0419 #> .. ..$ se : num 0.0199 #> .. ..$ pvalue : num 0.0355 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "Paget's disease" #> .. ..$ outID_mrbase: chr "975" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num -0.524 #> .. ..$ se : num 0.249 #> .. ..$ pvalue : num 0.0356 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "Fractured bone site(s): Other bones" #> .. ..$ outID_mrbase: chr "UKB-a:441" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num -0.104 #> .. ..$ se : num 0.0499 #> .. ..$ pvalue : num 0.0369 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "Diagnoses - main ICD10: K80 Cholelithiasis" #> .. ..$ outID_mrbase: chr "UKB-a:559" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num -0.177 #> .. ..$ se : num 0.0864 #> .. ..$ pvalue : num 0.0409 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "Systolic blood pressure automated reading" #> .. ..$ outID_mrbase: chr "UKB-a:360" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num -0.0211 #> .. ..$ se : num 0.0105 #> .. ..$ pvalue : num 0.0451 #> ..$ :List of 8 #> .. ..$ expID : chr "ADAM19" #> .. ..$ outID : chr "Diagnoses - main ICD10: N20 Calculus of kidney and ureter" #> .. ..$ outID_mrbase: chr "UKB-a:574" #> .. ..$ nsnp : int 1 #> .. ..$ method : chr "Wald ratio" #> .. ..$ beta : num -0.37 #> .. ..$ se : num 0.185 #> .. ..$ pvalue : num 0.0458