oa_table.md

Loading rebi

require(devtools)
install_github("rebi", "ropensci")
require(rebi)

list tables for an article

my.tables <- read_oa_table("PMC3364197")
summary(my.tables)

##      Length Class      Mode
## [1,]  4     data.frame list
## [2,] 13     data.frame list
## [3,]  4     data.frame list
## [4,]  6     data.frame list
## [5,]  4     data.frame list
## [6,]  7     data.frame list

Get Table 2

do.call("rbind",(my.tables[2]))

##    Nearby gene(s)     Marker ID    Impact/effect of variant Odds ratio
## 1             CFH  rs1061170  1                     p.Y402H       2.74
## 2                   rs800292  2                      p.I62V       2.43
## 3                  rs6677604  3      proxy for ΔCFHR3/CFHR1       2.19
## 4           ARMS2 rs10490924  4                      p.A69S       3.13
## 5             CFB  rs4151667  5                       p.L9H       2.82
## 6                   rs438999  6 proxy for rs641153 (p.R32Q)       2.31
## 7              C3  rs2230199  7                     p.R102G       1.52
## 8            APOE     rs7412  8                     p.R158C       1.41
## 9                   rs429358  9                     p.C112R       1.35
## 10       PLA2G12A  rs2285714 10  synonymous exonic, unknown       1.14
## 11           LIPC   rs493258 11 intergenic (36 kb upstream)       1.18
## 12                rs10468017 12 intergenic (46 kb upstream)       1.26
## 13     SYN3/TIMP3  rs9621532 13           intronic, unknown       1.58
##      95% CI1 P-value2 Non risk allele Risk allele3 Controls (N = 796)
## 1  2.36–3.18 1.66E−45               T            C              0.365
## 2  2.02–2.92 6.95E−23               A            G              0.761
## 3  1.82–2.64 1.42E−17               A            G              0.777
## 4  2.68–3.68 7.97E−54               G            T              0.189
## 5  1.90–4.28 1.41E−07               A            T              0.951
## 6  1.73–3.11 5.75E−09               C            T              0.915
## 7  1.29–1.80 4.71E−07               G            C              0.175
## 8  1.12–1.80 0.003613               C            T              0.079
## 9  1.09–1.69 0.006812               C            T              0.881
## 10 1.00–1.30  0.04839               C            T              0.409
## 11 1.04–1.35  0.01277               T            C              0.538
## 12 1.08–1.46 0.002992               T            C              0.707
## 13 1.09–2.30  0.01246               C            A               0.96
##    Cases (N = 986) AUC4 of variant correlation5
## 1            0.600           0.676             
## 2            0.888           0.606        0.150
## 3            0.884           0.590        0.203
## 4            0.441           0.684             
## 5            0.982           0.530             
## 6            0.962           0.542         0.01
## 7            0.245           0.556             
## 8            0.107           0.526             
## 9            0.908           0.528        0.783
## 10           0.443           0.523             
## 11           0.580           0.531             
## 12           0.751           0.536        0.367
## 13           0.974           0.512