mr(
exposure_trait = NULL,
outcome_trait = NULL,
pval_threshold = 1e-05,
mode = c("table", "raw")
)A trait name, e.g. "Body mass index",
leaving exposure_trait as NULL will return MR information
related to a specific outcome.
NOTE: exposure_trait and outcome_trait cannot be both NULL.
A trait name, e.g. "Coronary heart disease",
leaving outcome_trait as NULL will return MR information
related to a specific exposure_trait.
NOTE: exposure_trait and outcome_trait cannot be both NULL.
P-value threshold
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.
Data from GET /mr
# Returns a data frame
# \dontrun{
mr(exposure_trait = "Body mass index", outcome_trait = "Coronary heart disease")
#> # A tibble: 18 × 10
#> exposure.id exposure.trait outcome.id outcome.trait mr.b mr.se mr.pval
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 ieu-a-2 Body mass index ieu-a-7 Coronary hear… 0.464 0.0415 5.46e-29
#> 2 ebi-a-GCST0… Body mass index ieu-a-7 Coronary hear… 0.457 0.0410 3.33e-20
#> 3 ieu-a-974 Body mass index ieu-a-7 Coronary hear… 0.389 0.0493 3.42e-15
#> 4 ieu-a-835 Body mass index ieu-a-7 Coronary hear… 0.417 0.0492 1.00e-11
#> 5 ieu-a-974 Body mass index ieu-a-9 Coronary hear… 0.320 0.0536 2.32e- 9
#> 6 ieu-a-2 Body mass index ieu-a-9 Coronary hear… 0.358 0.0535 5.91e- 9
#> 7 ieu-a-835 Body mass index ieu-a-9 Coronary hear… 0.397 0.0604 1.79e- 8
#> 8 ebi-a-GCST0… Body mass index ieu-a-9 Coronary hear… 0.341 0.0590 1.24e- 7
#> 9 ieu-a-95 Body mass index ieu-a-9 Coronary hear… 0.371 0.0708 1.62e- 7
#> 10 ebi-a-GCST0… Body mass index ieu-a-6 Coronary hear… 0.493 0.0986 5.88e- 7
#> 11 ieu-a-785 Body mass index ieu-a-9 Coronary hear… 0.395 0.0609 1.07e- 6
#> 12 ebi-a-GCST0… Body mass index ebi-a-GCST… Coronary hear… 0.309 0.0648 1.81e- 6
#> 13 ebi-a-GCST0… Body mass index ieu-a-8 Coronary hear… 0.309 0.0648 1.81e- 6
#> 14 ebi-a-GCST0… Body mass index ieu-a-7 Coronary hear… 0.275 0.0514 2.76e- 6
#> 15 ieu-a-95 Body mass index ieu-a-7 Coronary hear… 0.455 0.0971 2.82e- 6
#> 16 ieu-a-2 Body mass index ieu-a-8 Coronary hear… 0.317 0.0686 3.93e- 6
#> 17 ieu-a-2 Body mass index ebi-a-GCST… Coronary hear… 0.312 0.0688 5.86e- 6
#> 18 ieu-a-974 Body mass index ieu-a-8 Coronary hear… 0.328 0.0731 6.97e- 6
#> # … with 3 more variables: mr.method <chr>, mr.selection <chr>,
#> # mr.moescore <dbl>
# }
# Returns raw response
# \dontrun{
mr(
exposure_trait = "Body mass index", outcome_trait = "Coronary heart disease",
mode = "raw"
) %>% str()
#> List of 2
#> $ metadata:List of 3
#> ..$ query : chr "MATCH (exposure:Gwas)-[mr:MR_EVE_MR]->(outcome:Gwas) WHERE exposure.trait = \"Body mass index\" AND outcome.tra"| __truncated__
#> ..$ total_seconds: num 0.0273
#> ..$ empty_results: logi FALSE
#> $ results :List of 18
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ieu-a-2"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-7"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.464
#> .. .. ..$ se : num 0.0415
#> .. .. ..$ pval : num 5.46e-29
#> .. .. ..$ method : chr "FE IVW"
#> .. .. ..$ selection: chr "HF"
#> .. .. ..$ moescore : num 0.91
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ebi-a-GCST006368"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-7"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.457
#> .. .. ..$ se : num 0.041
#> .. .. ..$ pval : num 3.33e-20
#> .. .. ..$ method : chr "RE IVW"
#> .. .. ..$ selection: chr "DF + HF"
#> .. .. ..$ moescore : num 0.92
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ieu-a-974"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-7"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.389
#> .. .. ..$ se : num 0.0493
#> .. .. ..$ pval : num 3.42e-15
#> .. .. ..$ method : chr "FE IVW"
#> .. .. ..$ selection: chr "DF"
#> .. .. ..$ moescore : num 0.89
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ieu-a-835"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-7"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.417
#> .. .. ..$ se : num 0.0492
#> .. .. ..$ pval : num 1e-11
#> .. .. ..$ method : chr "Simple mean"
#> .. .. ..$ selection: chr "HF"
#> .. .. ..$ moescore : num 0.96
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ieu-a-974"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-9"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.32
#> .. .. ..$ se : num 0.0536
#> .. .. ..$ pval : num 2.32e-09
#> .. .. ..$ method : chr "FE IVW"
#> .. .. ..$ selection: chr "DF + HF"
#> .. .. ..$ moescore : num 0.86
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ieu-a-2"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-9"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.358
#> .. .. ..$ se : num 0.0535
#> .. .. ..$ pval : num 5.91e-09
#> .. .. ..$ method : chr "RE IVW"
#> .. .. ..$ selection: chr "HF"
#> .. .. ..$ moescore : num 0.89
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ieu-a-835"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-9"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.397
#> .. .. ..$ se : num 0.0604
#> .. .. ..$ pval : num 1.79e-08
#> .. .. ..$ method : chr "RE IVW"
#> .. .. ..$ selection: chr "HF"
#> .. .. ..$ moescore : num 0.92
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ebi-a-GCST006368"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-9"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.341
#> .. .. ..$ se : num 0.059
#> .. .. ..$ pval : num 1.24e-07
#> .. .. ..$ method : chr "RE IVW"
#> .. .. ..$ selection: chr "HF"
#> .. .. ..$ moescore : num 0.84
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ieu-a-95"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-9"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.371
#> .. .. ..$ se : num 0.0708
#> .. .. ..$ pval : num 1.62e-07
#> .. .. ..$ method : chr "FE IVW"
#> .. .. ..$ selection: chr "HF"
#> .. .. ..$ moescore : num 0.75
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ebi-a-GCST006368"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-6"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.493
#> .. .. ..$ se : num 0.0986
#> .. .. ..$ pval : num 5.88e-07
#> .. .. ..$ method : chr "FE IVW"
#> .. .. ..$ selection: chr "DF + HF"
#> .. .. ..$ moescore : num 0.79
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ieu-a-785"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-9"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.395
#> .. .. ..$ se : num 0.0609
#> .. .. ..$ pval : num 1.07e-06
#> .. .. ..$ method : chr "RE IVW"
#> .. .. ..$ selection: chr "HF"
#> .. .. ..$ moescore : num 0.84
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ebi-a-GCST006368"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ebi-a-GCST000998"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.309
#> .. .. ..$ se : num 0.0648
#> .. .. ..$ pval : num 1.81e-06
#> .. .. ..$ method : chr "FE IVW"
#> .. .. ..$ selection: chr "Tophits"
#> .. .. ..$ moescore : num 0.82
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ebi-a-GCST006368"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-8"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.309
#> .. .. ..$ se : num 0.0648
#> .. .. ..$ pval : num 1.81e-06
#> .. .. ..$ method : chr "FE IVW"
#> .. .. ..$ selection: chr "Tophits"
#> .. .. ..$ moescore : num 0.81
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ebi-a-GCST004904"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-7"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.275
#> .. .. ..$ se : num 0.0514
#> .. .. ..$ pval : num 2.76e-06
#> .. .. ..$ method : chr "RE IVW"
#> .. .. ..$ selection: chr "DF + HF"
#> .. .. ..$ moescore : num 0.72
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ieu-a-95"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-7"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.455
#> .. .. ..$ se : num 0.0971
#> .. .. ..$ pval : num 2.82e-06
#> .. .. ..$ method : chr "Penalised median"
#> .. .. ..$ selection: chr "DF"
#> .. .. ..$ moescore : num 0.78
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ieu-a-2"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-8"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.317
#> .. .. ..$ se : num 0.0686
#> .. .. ..$ pval : num 3.93e-06
#> .. .. ..$ method : chr "FE IVW"
#> .. .. ..$ selection: chr "DF"
#> .. .. ..$ moescore : num 0.75
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ieu-a-2"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ebi-a-GCST000998"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.312
#> .. .. ..$ se : num 0.0688
#> .. .. ..$ pval : num 5.86e-06
#> .. .. ..$ method : chr "FE IVW"
#> .. .. ..$ selection: chr "DF"
#> .. .. ..$ moescore : num 0.76
#> ..$ :List of 3
#> .. ..$ exposure:List of 2
#> .. .. ..$ id : chr "ieu-a-974"
#> .. .. ..$ trait: chr "Body mass index"
#> .. ..$ outcome :List of 2
#> .. .. ..$ id : chr "ieu-a-8"
#> .. .. ..$ trait: chr "Coronary heart disease"
#> .. ..$ mr :List of 6
#> .. .. ..$ b : num 0.328
#> .. .. ..$ se : num 0.0731
#> .. .. ..$ pval : num 6.97e-06
#> .. .. ..$ method : chr "FE IVW"
#> .. .. ..$ selection: chr "DF"
#> .. .. ..$ moescore : num 0.85
# }
# Use a different threshold
# \dontrun{
mr(exposure_trait = "Body mass index", pval_threshold = 1e-8)
#> # A tibble: 2,138 × 10
#> exposure.id exposure.trait outcome.id outcome.trait mr.b mr.se mr.pval
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 ieu-a-974 Body mass index ebi-a-GCS… Fibrinogen lev… 0.193 0.00224 0
#> 2 ebi-a-GCST0… Body mass index ukb-b-2303 Body mass inde… 0.595 0.0153 0
#> 3 ieu-a-835 Body mass index ukb-b-180… Leg fat mass (… 0.608 0.0139 0
#> 4 ieu-a-835 Body mass index ukb-b-128… Arm fat percen… 0.526 0.0130 0
#> 5 ieu-a-835 Body mass index ieu-a-93 Overweight 1.67 0.0341 0
#> 6 ieu-a-835 Body mass index ieu-a-61 Waist circumfe… 0.824 0.0194 0
#> 7 ieu-a-835 Body mass index ieu-a-60 Waist circumfe… 0.820 0.0195 0
#> 8 ieu-a-2 Body mass index ukb-b-4650 Comparative bo… 0.439 0.00989 0
#> 9 ebi-a-GCST0… Body mass index ukb-b-201… Arm fat percen… 0.533 0.0104 0
#> 10 ieu-a-2 Body mass index ukb-b-2303 Body mass inde… 0.674 0.0178 0
#> # … with 2,128 more rows, and 3 more variables: mr.method <chr>,
#> # mr.selection <chr>, mr.moescore <dbl>
# }