library(DRrequired)
library(knitr)
opts_chunk$set(tidy = FALSE, out.width=".9\\paperwidth")
message('Comparing HR and RR for GMC and HUNK Gene\n')
## Comparing HR and RR for GMC and HUNK Gene
message('Windowing URL RR: https://wwwdev.ebi.ac.uk/mi/impc/dev/phenotype-archive/media/images/windowing/?alleleSymbol=Hunk%3Ctm1b(EUCOMM)Wtsi%3E&colonyID=H4884-EPD0822_3_A06-1&procedure=Electrocardiogram%20(ECG)%20%7C%20IMPC_ECG¶meter=RR%20%7C%20IMPC_ECG_004_001¢er=HMGU&zygosity=homozygote&metadata=1d0db8dd7f80ac3c47bb1c9e737fee90&version=DR8%7CResults_9.1')
## Windowing URL RR: https://wwwdev.ebi.ac.uk/mi/impc/dev/phenotype-archive/media/images/windowing/?alleleSymbol=Hunk%3Ctm1b(EUCOMM)Wtsi%3E&colonyID=H4884-EPD0822_3_A06-1&procedure=Electrocardiogram%20(ECG)%20%7C%20IMPC_ECG¶meter=RR%20%7C%20IMPC_ECG_004_001¢er=HMGU&zygosity=homozygote&metadata=1d0db8dd7f80ac3c47bb1c9e737fee90&version=DR8%7CResults_9.1
message('Windowing URL HR: https://wwwdev.ebi.ac.uk/mi/impc/dev/phenotype-archive/media/images/windowing/?alleleSymbol=Hunk%3Ctm1b(EUCOMM)Wtsi%3E&colonyID=H4884-EPD0822_3_A06-1&procedure=Electrocardiogram%20(ECG)%20%7C%20IMPC_ECG¶meter=HR%20%7C%20IMPC_ECG_002_001¢er=HMGU&zygosity=homozygote&metadata=1d0db8dd7f80ac3c47bb1c9e737fee90&version=DR9.1%7CResults_9.1')
## Windowing URL HR: https://wwwdev.ebi.ac.uk/mi/impc/dev/phenotype-archive/media/images/windowing/?alleleSymbol=Hunk%3Ctm1b(EUCOMM)Wtsi%3E&colonyID=H4884-EPD0822_3_A06-1&procedure=Electrocardiogram%20(ECG)%20%7C%20IMPC_ECG¶meter=HR%20%7C%20IMPC_ECG_002_001¢er=HMGU&zygosity=homozygote&metadata=1d0db8dd7f80ac3c47bb1c9e737fee90&version=DR9.1%7CResults_9.1
dfRR = read.csv(
file = UnzipAndfilePath(
'https://wwwdev.ebi.ac.uk/~hamedhm/windowing/DR9.1/jobs/Results_9.1/HMGU/IMPC_ECG/IMPC_ECG_004_001/H4884_EPD0822_3_A06_1/homozygote/1d0db8dd7f80ac3c47bb1c9e737fee90/output_rawData.csv.zip'
)[1]
)
## 2018-11-30 10:52:56. Unziping file ...
## 2018-11-30 10:52:56. Successfully unziped. List of files:
## 1 ==> C:\Users\hamedhm\AppData\Local\Temp\RtmpG6uknf/XWDP/output_rawData.csv
## 2 ==> C:\Users\hamedhm\AppData\Local\Temp\RtmpG6uknf/XWDP/ReadMe.txt
dfHR = read.csv(
file = UnzipAndfilePath(
'https://wwwdev.ebi.ac.uk/~hamedhm/windowing/DR9.1/jobs/Results_9.1/HMGU/IMPC_ECG/IMPC_ECG_002_001/H4884_EPD0822_3_A06_1/homozygote/1d0db8dd7f80ac3c47bb1c9e737fee90/output_rawData.csv.zip'
)[1]
)
## 2018-11-30 10:52:56. Unziping file ...
## 2018-11-30 10:52:56. Successfully unziped. List of files:
## 1 ==> C:\Users\hamedhm\AppData\Local\Temp\RtmpG6uknf/RFBJ/output_rawData.csv
## 2 ==> C:\Users\hamedhm\AppData\Local\Temp\RtmpG6uknf/RFBJ/ReadMe.txt
df = merge(dfRR, dfHR, by = 'external_sample_id')
dp = cbind(RR = df$data_point.x,
'HR->RR' = round(60 / df$data_point.y * 1000, 2),
HR = df$data_point.y,
external_sample_id=df$external_sample_id)
f = function(dp,
er = 2,
col = 2,
...) {
outliers = dp[abs(dp[, 1] - dp[, 2]) > er,,drop=FALSE]
plot(dp, sub = paste0('Total = ',nrow(outliers)),...)
points(
outliers[, 1],
outliers[, 2],
col = col,
pch = 5,
lwd = 3,
cex = 3
)
print(outliers)
}
f(dp, .25, col = 2 , main = '(deviation of RR from HR->RR) greater than 0.25')
## RR HR->RR HR external_sample_id
## [1,] 88.4 88.11 681 30254295
## [2,] 91.1 90.50 663 30261447
## [3,] 88.6 88.24 680 30261589
## [4,] 121.3 103.27 581 30262136
## [5,] 80.7 79.26 757 30262142
## [6,] 78.6 78.33 766 30266731
## [7,] 110.5 109.69 547 30274858
## [8,] 82.9 80.65 744 30278932
## [9,] 85.8 83.10 722 30279621
## [10,] 89.9 89.55 670 30293602
## [11,] 83.0 82.64 726 30297710
## [12,] 76.3 75.57 794 30299711
## [13,] 81.9 81.63 735 30300381
## [14,] 78.9 78.64 763 30300391
## [15,] 86.1 85.47 702 30301654
## [16,] 74.8 74.07 810 30302238
## [17,] 82.3 81.97 732 30306113
## [18,] 85.9 85.59 701 30308340
## [19,] 87.6 86.96 690 30309631
## [20,] 92.4 91.05 659 30313887
## [21,] 80.7 80.32 747 30314784
## [22,] 97.1 96.46 622 30317673
## [23,] 76.2 75.47 795 30318194
## [24,] 80.3 80.00 750 30319194
## [25,] 81.9 81.63 735 30320448
## [26,] 84.2 83.92 715 30321058
## [27,] 97.2 96.93 619 30328730
## [28,] 81.3 78.33 766 30328740
## [29,] 86.1 85.71 700 30329534
## [30,] 85.6 85.23 704 30329535
## [31,] 100.9 100.17 599 30330000
## [32,] 92.0 91.32 657 30331292
## [33,] 74.1 73.53 816 30334754
## [34,] 79.2 78.84 761 30335462
## [35,] 85.5 84.39 711 30336085
## [36,] 80.3 80.00 750 30338352
## [37,] 78.9 76.82 781 30340049
## [38,] 85.3 84.99 706 30340749
## [39,] 86.4 86.08 697 30346116
## [40,] 79.4 78.23 767 30346119
## [41,] 74.0 73.53 816 30347238
## [42,] 91.3 83.80 716 30347353
## [43,] 83.9 83.45 719 30349452
## [44,] 79.0 75.00 800 30349455
## [45,] 81.2 80.54 745 30349458
## [46,] 84.6 84.15 713 30351279
## [47,] 74.8 74.53 805 30353328
## [48,] 87.3 86.46 694 30355559
## [49,] 86.6 86.33 695 30357652
## [50,] 74.0 73.62 815 30359756
## [51,] 86.0 85.71 700 30362449
## [52,] 82.3 81.97 732 30362470
## [53,] 78.3 77.82 771 30363357
## [54,] 80.3 79.68 753 30367669
## [55,] 78.9 78.53 764 30368953
## [56,] 79.6 78.02 769 30368961
## [57,] 76.4 75.57 794 30368962
## [58,] 79.8 78.64 763 30368964
## [59,] 78.0 77.22 777 30370946
## [60,] 77.4 77.02 779 30372443
## [61,] 78.9 78.53 764 30376913
## [62,] 84.3 84.03 714 30377419
## [63,] 78.3 77.92 770 30385985
## [64,] 85.2 84.51 710 30389470
## [65,] 80.8 79.05 759 30394140
## [66,] 75.5 74.44 806 30395734
f(dp, 1 , col = 3 , main = '(deviation of RR from HR->RR) greater than 1')
## RR HR->RR HR external_sample_id
## [1,] 121.3 103.27 581 30262136
## [2,] 80.7 79.26 757 30262142
## [3,] 82.9 80.65 744 30278932
## [4,] 85.8 83.10 722 30279621
## [5,] 92.4 91.05 659 30313887
## [6,] 81.3 78.33 766 30328740
## [7,] 85.5 84.39 711 30336085
## [8,] 78.9 76.82 781 30340049
## [9,] 79.4 78.23 767 30346119
## [10,] 91.3 83.80 716 30347353
## [11,] 79.0 75.00 800 30349455
## [12,] 79.6 78.02 769 30368961
## [13,] 79.8 78.64 763 30368964
## [14,] 80.8 79.05 759 30394140
## [15,] 75.5 74.44 806 30395734
f(dp, 2 , col = 4 , main = '(deviation of RR from HR->RR) greater than 3')
## RR HR->RR HR external_sample_id
## [1,] 121.3 103.27 581 30262136
## [2,] 82.9 80.65 744 30278932
## [3,] 85.8 83.10 722 30279621
## [4,] 81.3 78.33 766 30328740
## [5,] 78.9 76.82 781 30340049
## [6,] 91.3 83.80 716 30347353
## [7,] 79.0 75.00 800 30349455
f(dp, 5 , col = 5 , main = '(deviation of RR from HR->RR) greater than 5')
## RR HR->RR HR external_sample_id
## [1,] 121.3 103.27 581 30262136
## [2,] 91.3 83.80 716 30347353
f(dp, 18, col = 6 , main = '(deviation of RR from HR->RR) greater than 18!')
## RR HR->RR HR external_sample_id
## [1,] 121.3 103.27 581 30262136
cor(dp[,1:2])
## RR HR->RR
## RR 1.0000000 0.9905745
## HR->RR 0.9905745 1.0000000