Genomic Data Analysis Assessment
Ishani Ray
2025-10-19
#Install maftools in R
# Install BiocManager if needed
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# Install maftools
BiocManager::install("maftools")##Q6: Load and Summarize MAF File
library(maftools)
# View available TCGA cohorts
tcgaAvailable()# Load LGG cohort
lgg <- tcgaLoad(study = "LGG")
# View summary
lgg## An object of class MAF
## ID summary Mean Median
## <char> <char> <num> <num>
## 1: NCBI_Build GRCh37 NA NA
## 2: Center MC3_LGG NA NA
## 3: Samples 525 NA NA
## 4: nGenes 11767 NA NA
## 5: Frame_Shift_Del 921 1.754 1
## 6: Frame_Shift_Ins 325 0.619 0
## 7: In_Frame_Del 372 0.709 0
## 8: In_Frame_Ins 14 0.027 0
## 9: Missense_Mutation 24953 47.530 23
## 10: Nonsense_Mutation 1729 3.293 1
## 11: Nonstop_Mutation 18 0.034 0
## 12: Splice_Site 728 1.387 0
## 13: Translation_Start_Site 39 0.074 0
## 14: total 29099 55.427 28# Get median variants per sample
sample_summary <- getSampleSummary(lgg)
colnames(sample_summary)## [1] "Tumor_Sample_Barcode" "Frame_Shift_Del" "Frame_Shift_Ins"
## [4] "In_Frame_Del" "In_Frame_Ins" "Missense_Mutation"
## [7] "Nonsense_Mutation" "Nonstop_Mutation" "Splice_Site"
## [10] "Translation_Start_Site" "total"head(sample_summary)total_variants <- sample_summary$total
total_variants## [1] 10772 1591 451 440 289 110 104 84 84 82 75 74
## [13] 73 72 68 65 64 63 62 62 62 61 61 60
## [25] 60 59 59 58 58 58 58 57 57 57 57 56
## [37] 56 56 55 55 54 54 54 53 51 51 51 51
## [49] 51 50 50 50 50 49 49 49 49 49 48 48
## [61] 48 48 48 47 47 47 47 47 47 47 47 46
## [73] 46 46 45 45 45 45 45 45 44 44 44 44
## [85] 44 44 43 43 43 43 43 43 43 43 42 42
## [97] 42 41 41 41 41 40 40 40 40 40 40 40
## [109] 39 39 39 39 39 39 39 39 39 39 39 39
## [121] 38 38 38 38 38 38 38 38 37 37 37 37
## [133] 37 37 37 37 36 36 36 36 36 36 36 36
## [145] 36 36 36 36 36 36 36 36 36 36 36 36
## [157] 35 35 35 35 35 35 35 35 35 35 35 35
## [169] 35 35 35 35 35 35 35 34 34 34 34 34
## [181] 34 34 34 34 33 33 33 33 33 33 33 33
## [193] 33 33 33 33 33 33 33 32 32 32 32 32
## [205] 32 32 32 32 31 31 31 31 31 31 31 31
## [217] 31 31 31 31 30 30 30 30 30 30 30 30
## [229] 30 30 30 30 30 30 30 29 29 29 29 29
## [241] 29 29 29 29 29 29 29 29 29 29 29 29
## [253] 28 28 28 28 28 28 28 28 28 28 28 28
## [265] 28 28 27 27 27 27 27 27 27 27 27 27
## [277] 27 27 27 27 26 26 26 26 26 26 26 26
## [289] 26 26 26 26 26 26 26 26 26 26 26 25
## [301] 25 25 25 25 25 25 25 25 25 25 25 25
## [313] 25 25 25 25 25 25 25 25 25 25 24 24
## [325] 24 24 24 24 24 24 24 24 24 24 24 24
## [337] 24 24 24 24 24 24 24 23 23 23 23 23
## [349] 23 23 23 23 23 23 23 22 22 22 22 22
## [361] 22 22 22 22 22 22 22 22 22 22 22 22
## [373] 22 22 22 22 22 22 21 21 21 21 21 21
## [385] 21 21 21 21 21 21 21 21 21 20 20 20
## [397] 20 20 20 20 20 20 20 20 19 19 19 19
## [409] 19 19 19 19 19 19 18 18 18 18 18 18
## [421] 18 18 18 18 18 18 18 18 18 18 17 17
## [433] 17 17 17 17 17 17 17 17 17 17 17 16
## [445] 16 16 16 16 16 16 16 16 16 16 16 16
## [457] 15 15 15 15 15 15 15 15 15 14 14 14
## [469] 14 14 14 14 14 14 14 13 13 13 13 13
## [481] 13 13 13 13 13 13 13 13 12 12 12 11
## [493] 11 11 11 11 10 10 10 10 10 9 9 9
## [505] 9 8 8 8 8 8 7 7 6 5 5 5
## [517] 5 3 2 2 2 1 1 1 0median(total_variants)## [1] 28#Generate Required Plots
##1. Oncoplot of Top 5 Mutated Genes
# Generate oncoplot
# Set directory
out_dir <- "C:/Users/isr4005/OneDrive - Oklahoma A and M System/extra 2/extra/Desktop"
png(filename = file.path(out_dir, "oncoplot_top5.png"), width = 10, height = 8, units = "in", res = 300)
oncoplot(maf = lgg, top = 5)
dev.off()## png
## 2oncoplot(maf = lgg, top = 5)
###2. Transition/Transversion Ratio Boxplot
# Generate Ti/Tv plot
png(file.path(out_dir, "titv_boxplot.png"), width = 8, height = 6, units = "in", res = 300)
lgg_titv <- titv(maf = lgg, plot = TRUE, useSyn = TRUE)
dev.off() ## png
## 2titv(maf = lgg, plot = TRUE, useSyn = TRUE)
## $fraction.contribution
## Key: <Tumor_Sample_Barcode>
## Tumor_Sample_Barcode C>A C>G C>T T>C
## <fctr> <num> <num> <num> <num>
## 1: TCGA-CS-4938-01B-11D-1893-08 13.636364 13.636364 40.90909 18.181818
## 2: TCGA-CS-4941-01A-01D-1468-08 3.389831 6.779661 66.10169 5.084746
## 3: TCGA-CS-4942-01A-01D-1468-08 8.108108 10.810811 54.05405 24.324324
## 4: TCGA-CS-4943-01A-01D-1468-08 2.631579 13.157895 47.36842 23.684211
## 5: TCGA-CS-4944-01A-01D-1468-08 18.181818 4.545455 31.81818 40.909091
## ---
## 521: TCGA-WY-A85A-01A-21D-A36O-08 12.500000 0.000000 75.00000 6.250000
## 522: TCGA-WY-A85B-01A-11D-A36O-08 11.764706 11.764706 58.82353 17.647059
## 523: TCGA-WY-A85C-01A-11D-A36O-08 11.764706 8.823529 47.05882 20.588235
## 524: TCGA-WY-A85D-01A-11D-A36O-08 6.521739 10.869565 47.82609 23.913043
## 525: TCGA-WY-A85E-01A-11D-A36O-08 14.457831 7.228916 40.96386 20.481928
## T>A T>G
## <num> <num>
## 1: 4.545455 9.090909
## 2: 11.864407 6.779661
## 3: 2.702703 0.000000
## 4: 7.894737 5.263158
## 5: 4.545455 0.000000
## ---
## 521: 0.000000 6.250000
## 522: 0.000000 0.000000
## 523: 5.882353 5.882353
## 524: 4.347826 6.521739
## 525: 9.638554 7.228916
##
## $raw.counts
## Key: <Tumor_Sample_Barcode>
## Tumor_Sample_Barcode C>A C>G C>T T>C T>A T>G
## <fctr> <int> <int> <int> <int> <int> <int>
## 1: TCGA-CS-4938-01B-11D-1893-08 3 3 9 4 1 2
## 2: TCGA-CS-4941-01A-01D-1468-08 2 4 39 3 7 4
## 3: TCGA-CS-4942-01A-01D-1468-08 3 4 20 9 1 0
## 4: TCGA-CS-4943-01A-01D-1468-08 1 5 18 9 3 2
## 5: TCGA-CS-4944-01A-01D-1468-08 4 1 7 9 1 0
## ---
## 521: TCGA-WY-A85A-01A-21D-A36O-08 2 0 12 1 0 1
## 522: TCGA-WY-A85B-01A-11D-A36O-08 2 2 10 3 0 0
## 523: TCGA-WY-A85C-01A-11D-A36O-08 4 3 16 7 2 2
## 524: TCGA-WY-A85D-01A-11D-A36O-08 3 5 22 11 2 3
## 525: TCGA-WY-A85E-01A-11D-A36O-08 12 6 34 17 8 6
##
## $TiTv.fractions
## Tumor_Sample_Barcode Ti Tv
## 1 TCGA-CS-4938-01B-11D-1893-08 59.090909 40.909091
## 2 TCGA-CS-4941-01A-01D-1468-08 71.186441 28.813559
## 3 TCGA-CS-4942-01A-01D-1468-08 78.378378 21.621622
## 4 TCGA-CS-4943-01A-01D-1468-08 71.052632 28.947368
## 5 TCGA-CS-4944-01A-01D-1468-08 72.727273 27.272727
## 6 TCGA-CS-5390-01A-02D-1468-08 64.705882 35.294118
## 7 TCGA-CS-5393-01A-01D-1468-08 74.285714 25.714286
## 8 TCGA-CS-5394-01A-01D-1468-08 76.923077 23.076923
## 9 TCGA-CS-5395-01A-01D-1468-08 70.909091 29.090909
## 10 TCGA-CS-5396-01A-02D-1468-08 69.230769 30.769231
## 11 TCGA-CS-5397-01A-01D-1893-08 64.814815 35.185185
## 12 TCGA-CS-6186-01A-12D-2024-08 72.222222 27.777778
## 13 TCGA-CS-6188-01A-11D-1893-08 76.785714 23.214286
## 14 TCGA-CS-6290-01A-11D-1705-08 61.538462 38.461538
## 15 TCGA-CS-6665-01A-11D-1893-08 67.777778 32.222222
## 16 TCGA-CS-6666-01A-11D-1893-08 58.490566 41.509434
## 17 TCGA-CS-6667-01A-12D-2024-08 75.000000 25.000000
## 18 TCGA-CS-6668-01A-11D-1893-08 83.870968 16.129032
## 19 TCGA-CS-6669-01A-11D-1893-08 0.000000 100.000000
## 20 TCGA-CS-6670-01A-11D-1893-08 82.978723 17.021277
## 21 TCGA-DB-5270-01A-02D-1468-08 58.064516 41.935484
## 22 TCGA-DB-5273-01A-01D-1468-08 78.947368 21.052632
## 23 TCGA-DB-5274-01A-01D-1468-08 73.584906 26.415094
## 24 TCGA-DB-5275-01A-01D-1468-08 60.975610 39.024390
## 25 TCGA-DB-5276-01A-01D-1468-08 76.470588 23.529412
## 26 TCGA-DB-5277-01A-01D-1468-08 71.698113 28.301887
## 27 TCGA-DB-5278-01A-01D-1468-08 50.000000 50.000000
## 28 TCGA-DB-5279-01A-01D-1468-08 84.375000 15.625000
## 29 TCGA-DB-5280-01A-01D-1468-08 68.965517 31.034483
## 30 TCGA-DB-5281-01A-01D-1468-08 71.875000 28.125000
## 31 TCGA-DB-A4X9-01A-11D-A26M-08 75.000000 25.000000
## 32 TCGA-DB-A4XA-01A-11D-A26M-08 66.666667 33.333333
## 33 TCGA-DB-A4XB-01A-11D-A26M-08 65.789474 34.210526
## 34 TCGA-DB-A4XC-01A-11D-A26M-08 64.705882 35.294118
## 35 TCGA-DB-A4XD-01A-11D-A27K-08 78.378378 21.621622
## 36 TCGA-DB-A4XE-01A-11D-A27K-08 54.838710 45.161290
## 37 TCGA-DB-A4XF-01A-11D-A27K-08 77.777778 22.222222
## 38 TCGA-DB-A4XG-01A-11D-A27K-08 76.923077 23.076923
## 39 TCGA-DB-A4XH-01A-11D-A27K-08 80.000000 20.000000
## 40 TCGA-DB-A64L-01A-11D-A29Q-08 76.842105 23.157895
## 41 TCGA-DB-A64O-01A-11D-A29Q-08 68.965517 31.034483
## 42 TCGA-DB-A64P-01A-11D-A29Q-08 61.290323 38.709677
## 43 TCGA-DB-A64Q-01A-11D-A29Q-08 80.000000 20.000000
## 44 TCGA-DB-A64R-01A-11D-A29Q-08 70.588235 29.411765
## 45 TCGA-DB-A64S-01A-11D-A29Q-08 53.846154 46.153846
## 46 TCGA-DB-A64U-01A-11D-A29Q-08 75.000000 25.000000
## 47 TCGA-DB-A64V-01A-11D-A29Q-08 84.210526 15.789474
## 48 TCGA-DB-A64W-01A-11D-A29Q-08 77.358491 22.641509
## 49 TCGA-DB-A64X-01A-11D-A29Q-08 75.257732 24.742268
## 50 TCGA-DB-A75K-01A-11D-A32B-08 61.363636 38.636364
## 51 TCGA-DB-A75L-01A-11D-A32B-08 70.212766 29.787234
## 52 TCGA-DB-A75M-01A-11D-A32B-08 62.068966 37.931034
## 53 TCGA-DB-A75O-01A-11D-A32B-08 64.705882 35.294118
## 54 TCGA-DB-A75P-01A-11D-A32B-08 83.333333 16.666667
## 55 TCGA-DH-5140-01A-01D-1468-08 72.727273 27.272727
## 56 TCGA-DH-5141-01A-01D-1468-08 81.250000 18.750000
## 57 TCGA-DH-5142-01A-01D-1468-08 68.750000 31.250000
## 58 TCGA-DH-5143-01A-01D-1468-08 68.571429 31.428571
## 59 TCGA-DH-5144-01A-01D-1468-08 82.692308 17.307692
## 60 TCGA-DH-A669-01A-12D-A31L-08 78.787879 21.212121
## 61 TCGA-DH-A669-02A-11D-A31L-08 69.444444 30.555556
## 62 TCGA-DH-A66B-01A-11D-A29Q-08 63.043478 36.956522
## 63 TCGA-DH-A66D-01A-11D-A31L-08 61.224490 38.775510
## 64 TCGA-DH-A66F-01A-11D-A29Q-08 90.909091 9.090909
## 65 TCGA-DH-A66G-01A-21D-A31L-08 64.285714 35.714286
## 66 TCGA-DH-A7UR-01A-11D-A33T-08 72.602740 27.397260
## 67 TCGA-DH-A7US-01A-11D-A33T-08 80.952381 19.047619
## 68 TCGA-DH-A7UT-01A-12D-A34A-08 61.538462 38.461538
## 69 TCGA-DH-A7UU-01A-12D-A34A-08 50.000000 50.000000
## 70 TCGA-DH-A7UV-01A-12D-A34A-08 68.421053 31.578947
## 71 TCGA-DU-5847-01A-11D-1705-08 62.000000 38.000000
## 72 TCGA-DU-5849-01A-11D-1705-08 73.913043 26.086957
## 73 TCGA-DU-5851-01A-13D-1893-08 53.125000 46.875000
## 74 TCGA-DU-5852-01A-11D-1705-08 81.052632 18.947368
## 75 TCGA-DU-5853-01A-11D-1893-08 56.521739 43.478261
## 76 TCGA-DU-5854-01A-11D-1705-08 76.363636 23.636364
## 77 TCGA-DU-5855-01A-11D-1705-08 77.777778 22.222222
## 78 TCGA-DU-5870-01A-11D-1705-08 78.947368 21.052632
## 79 TCGA-DU-5870-02A-12D-A36O-08 61.224490 38.775510
## 80 TCGA-DU-5871-01A-12D-1705-08 68.421053 31.578947
## 81 TCGA-DU-5872-01A-11D-1705-08 68.571429 31.428571
## 82 TCGA-DU-5872-02A-21D-A36O-08 66.666667 33.333333
## 83 TCGA-DU-5874-01A-11D-1705-08 82.758621 17.241379
## 84 TCGA-DU-6392-01A-11D-1705-08 70.763929 29.236071
## 85 TCGA-DU-6393-01A-11D-1705-08 78.947368 21.052632
## 86 TCGA-DU-6394-01A-11D-1705-08 65.384615 34.615385
## 87 TCGA-DU-6395-01A-12D-1705-08 66.666667 33.333333
## 88 TCGA-DU-6396-01A-11D-1705-08 67.924528 32.075472
## 89 TCGA-DU-6397-01A-11D-1705-08 48.484848 51.515152
## 90 TCGA-DU-6397-02A-12D-A36O-08 68.750000 31.250000
## 91 TCGA-DU-6399-01A-12D-1705-08 75.714286 24.285714
## 92 TCGA-DU-6400-01A-12D-1705-08 81.481481 18.518519
## 93 TCGA-DU-6401-01A-11D-1705-08 83.333333 16.666667
## 94 TCGA-DU-6402-01A-11D-1705-08 73.770492 26.229508
## 95 TCGA-DU-6403-01A-11D-1705-08 73.333333 26.666667
## 96 TCGA-DU-6404-01A-11D-1705-08 68.750000 31.250000
## 97 TCGA-DU-6404-02B-11D-A36O-08 48.181818 51.818182
## 98 TCGA-DU-6405-01A-11D-1705-08 80.000000 20.000000
## 99 TCGA-DU-6406-01A-11D-1705-08 80.000000 20.000000
## 100 TCGA-DU-6407-01A-13D-1705-08 75.757576 24.242424
## 101 TCGA-DU-6407-02B-11D-A36O-08 98.858447 1.141553
## 102 TCGA-DU-6408-01A-11D-1705-08 68.750000 31.250000
## 103 TCGA-DU-6410-01A-11D-1893-08 84.615385 15.384615
## 104 TCGA-DU-6542-01A-11D-1893-08 61.290323 38.709677
## 105 TCGA-DU-7006-01A-11D-2024-08 74.025974 25.974026
## 106 TCGA-DU-7007-01A-11D-2024-08 69.387755 30.612245
## 107 TCGA-DU-7008-01A-11D-2024-08 73.809524 26.190476
## 108 TCGA-DU-7009-01A-11D-2024-08 69.230769 30.769231
## 109 TCGA-DU-7010-01A-11D-2024-08 61.403509 38.596491
## 110 TCGA-DU-7011-01A-11D-2024-08 80.952381 19.047619
## 111 TCGA-DU-7012-01A-11D-2024-08 84.210526 15.789474
## 112 TCGA-DU-7013-01A-11D-2024-08 68.627451 31.372549
## 113 TCGA-DU-7015-01A-11D-2024-08 80.555556 19.444444
## 114 TCGA-DU-7018-01A-11D-2024-08 66.666667 33.333333
## 115 TCGA-DU-7019-01A-11D-2024-08 78.947368 21.052632
## 116 TCGA-DU-7290-01A-11D-2024-08 70.731707 29.268293
## 117 TCGA-DU-7292-01A-11D-2024-08 72.580645 27.419355
## 118 TCGA-DU-7294-01A-11D-2024-08 4.000000 96.000000
## 119 TCGA-DU-7298-01A-11D-2024-08 7.371007 92.628993
## 120 TCGA-DU-7299-01A-21D-2024-08 82.142857 17.857143
## 121 TCGA-DU-7300-01A-21D-2086-08 74.418605 25.581395
## 122 TCGA-DU-7301-01A-11D-2086-08 78.125000 21.875000
## 123 TCGA-DU-7302-01A-11D-2086-08 75.757576 24.242424
## 124 TCGA-DU-7304-01A-12D-2086-08 77.777778 22.222222
## 125 TCGA-DU-7304-02A-12D-A36O-08 60.784314 39.215686
## 126 TCGA-DU-7306-01A-11D-2086-08 57.894737 42.105263
## 127 TCGA-DU-7309-01A-11D-2086-08 65.306122 34.693878
## 128 TCGA-DU-8158-01A-11D-2253-08 58.333333 41.666667
## 129 TCGA-DU-8161-01A-11D-2253-08 67.857143 32.142857
## 130 TCGA-DU-8162-01A-21D-2253-08 74.285714 25.714286
## 131 TCGA-DU-8163-01A-11D-2253-08 70.833333 29.166667
## 132 TCGA-DU-8164-01A-11D-2253-08 62.790698 37.209302
## 133 TCGA-DU-8165-01A-11D-2253-08 51.136364 48.863636
## 134 TCGA-DU-8166-01A-11D-2253-08 58.333333 41.666667
## 135 TCGA-DU-8167-01A-11D-2253-08 83.950617 16.049383
## 136 TCGA-DU-8168-01A-11D-2253-08 73.770492 26.229508
## 137 TCGA-DU-A5TP-01A-11D-A289-08 72.222222 27.777778
## 138 TCGA-DU-A5TR-01A-11D-A289-08 68.750000 31.250000
## 139 TCGA-DU-A5TS-01A-11D-A289-08 78.260870 21.739130
## 140 TCGA-DU-A5TT-01A-11D-A289-08 72.058824 27.941176
## 141 TCGA-DU-A5TU-01A-11D-A289-08 70.689655 29.310345
## 142 TCGA-DU-A5TW-01A-11D-A289-08 77.419355 22.580645
## 143 TCGA-DU-A5TY-01A-11D-A289-08 77.941176 22.058824
## 144 TCGA-DU-A6S2-01A-21D-A32B-08 89.473684 10.526316
## 145 TCGA-DU-A6S3-01A-12D-A32B-08 90.000000 10.000000
## 146 TCGA-DU-A6S6-01A-21D-A32B-08 64.705882 35.294118
## 147 TCGA-DU-A6S7-01A-21D-A32B-08 75.675676 24.324324
## 148 TCGA-DU-A6S8-01A-12D-A32B-08 85.483871 14.516129
## 149 TCGA-DU-A76K-01A-11D-A33T-08 79.104478 20.895522
## 150 TCGA-DU-A76L-01A-11D-A32B-08 83.673469 16.326531
## 151 TCGA-DU-A76O-01A-11D-A32B-08 73.529412 26.470588
## 152 TCGA-DU-A76R-01A-11D-A32B-08 86.538462 13.461538
## 153 TCGA-DU-A7T6-01A-11D-A33T-08 49.629630 50.370370
## 154 TCGA-DU-A7T8-01A-21D-A34J-08 76.190476 23.809524
## 155 TCGA-DU-A7TA-01A-11D-A33T-08 51.351351 48.648649
## 156 TCGA-DU-A7TB-01A-11D-A33T-08 74.358974 25.641026
## 157 TCGA-DU-A7TC-01A-21D-A34J-08 75.757576 24.242424
## 158 TCGA-DU-A7TD-01A-12D-A34A-08 79.629630 20.370370
## 159 TCGA-DU-A7TG-01A-21D-A34J-08 92.307692 7.692308
## 160 TCGA-DU-A7TJ-01A-11D-A34J-08 68.965517 31.034483
## 161 TCGA-E1-5302-01A-01D-1468-08 79.545455 20.454545
## 162 TCGA-E1-5303-01A-01D-1468-08 58.823529 41.176471
## 163 TCGA-E1-5304-01A-01D-1468-08 60.526316 39.473684
## 164 TCGA-E1-5305-01A-01D-1893-08 81.481481 18.518519
## 165 TCGA-E1-5307-01A-01D-1893-08 76.744186 23.255814
## 166 TCGA-E1-5311-01A-01D-1468-08 78.260870 21.739130
## 167 TCGA-E1-5318-01A-01D-1468-08 68.750000 31.250000
## 168 TCGA-E1-5319-01A-01D-1893-08 81.395349 18.604651
## 169 TCGA-E1-5322-01A-01D-1468-08 79.411765 20.588235
## 170 TCGA-E1-A7YD-01A-11D-A34A-08 65.333333 34.666667
## 171 TCGA-E1-A7YE-01A-11D-A34A-08 43.333333 56.666667
## 172 TCGA-E1-A7YH-01A-11D-A34A-08 91.428571 8.571429
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## 429 TCGA-S9-A6U8-01A-21D-A33T-08 79.166667 20.833333
## 430 TCGA-S9-A6U9-01A-11D-A32B-08 76.923077 23.076923
## 431 TCGA-S9-A6UA-01A-12D-A33T-08 74.468085 25.531915
## 432 TCGA-S9-A6UB-01A-21D-A33T-08 91.176471 8.823529
## 433 TCGA-S9-A6WD-01A-12D-A33T-08 72.093023 27.906977
## 434 TCGA-S9-A6WE-01A-12D-A33T-08 100.000000 0.000000
## 435 TCGA-S9-A6WG-01A-11D-A33T-08 78.571429 21.428571
## 436 TCGA-S9-A6WH-01A-12D-A33T-08 71.276596 28.723404
## 437 TCGA-S9-A6WI-01A-21D-A33T-08 77.419355 22.580645
## 438 TCGA-S9-A6WL-01A-21D-A33T-08 74.000000 26.000000
## 439 TCGA-S9-A6WM-01A-12D-A33T-08 79.710145 20.289855
## 440 TCGA-S9-A6WN-01A-12D-A33T-08 86.842105 13.157895
## 441 TCGA-S9-A6WO-01A-21D-A34A-08 77.142857 22.857143
## 442 TCGA-S9-A6WP-01A-12D-A34A-08 81.818182 18.181818
## 443 TCGA-S9-A6WQ-01A-12D-A34A-08 76.086957 23.913043
## 444 TCGA-S9-A7IQ-01A-21D-A34A-08 94.736842 5.263158
## 445 TCGA-S9-A7IS-01A-11D-A34A-08 72.131148 27.868852
## 446 TCGA-S9-A7IX-01A-12D-A34A-08 69.444444 30.555556
## 447 TCGA-S9-A7IY-01A-11D-A34A-08 73.076923 26.923077
## 448 TCGA-S9-A7IZ-01A-11D-A34A-08 61.538462 38.461538
## 449 TCGA-S9-A7J0-01A-11D-A34A-08 76.000000 24.000000
## 450 TCGA-S9-A7J1-01A-21D-A34J-08 62.500000 37.500000
## 451 TCGA-S9-A7J2-01A-11D-A34A-08 83.333333 16.666667
## 452 TCGA-S9-A7J3-01A-21D-A34J-08 84.375000 15.625000
## 453 TCGA-S9-A7QW-01A-11D-A34A-08 73.333333 26.666667
## 454 TCGA-S9-A7QX-01A-11D-A34A-08 68.750000 31.250000
## 455 TCGA-S9-A7QY-01A-11D-A34A-08 78.947368 21.052632
## 456 TCGA-S9-A7QZ-01A-12D-A34J-08 65.217391 34.782609
## 457 TCGA-S9-A7R1-01A-12D-A34J-08 90.000000 10.000000
## 458 TCGA-S9-A7R2-01A-21D-A34J-08 60.714286 39.285714
## 459 TCGA-S9-A7R3-01A-11D-A34J-08 80.645161 19.354839
## 460 TCGA-S9-A7R4-01A-12D-A34J-08 65.625000 34.375000
## 461 TCGA-S9-A7R7-01A-11D-A34J-08 88.000000 12.000000
## 462 TCGA-S9-A7R8-01A-11D-A34J-08 73.809524 26.190476
## 463 TCGA-S9-A89V-01A-11D-A36O-08 76.470588 23.529412
## 464 TCGA-S9-A89Z-01A-11D-A36O-08 68.571429 31.428571
## 465 TCGA-TM-A7C3-01A-11D-A32B-08 84.615385 15.384615
## 466 TCGA-TM-A7C4-01A-11D-A32B-08 68.085106 31.914894
## 467 TCGA-TM-A7C5-01A-11D-A32B-08 77.777778 22.222222
## 468 TCGA-TM-A7CA-01A-21D-A33T-08 68.421053 31.578947
## 469 TCGA-TM-A7CF-01A-11D-A32B-08 65.000000 35.000000
## 470 TCGA-TM-A7CF-02A-11D-A32B-08 56.000000 44.000000
## 471 TCGA-TM-A84B-01A-11D-A36O-08 86.956522 13.043478
## 472 TCGA-TM-A84C-01A-11D-A36O-08 65.000000 35.000000
## 473 TCGA-TM-A84F-01A-11D-A36O-08 75.000000 25.000000
## 474 TCGA-TM-A84G-01A-11D-A36O-08 75.675676 24.324324
## 475 TCGA-TM-A84H-01A-11D-A36O-08 72.916667 27.083333
## 476 TCGA-TM-A84I-01A-11D-A36O-08 72.093023 27.906977
## 477 TCGA-TM-A84J-01A-11D-A36O-08 81.132075 18.867925
## 478 TCGA-TM-A84L-01A-11D-A36O-08 84.000000 16.000000
## 479 TCGA-TM-A84M-01A-11D-A36O-08 86.111111 13.888889
## 480 TCGA-TM-A84O-01A-11D-A36O-08 80.645161 19.354839
## 481 TCGA-TM-A84Q-01A-11D-A36O-08 61.111111 38.888889
## 482 TCGA-TM-A84R-01A-21D-A36O-08 85.714286 14.285714
## 483 TCGA-TM-A84S-01A-11D-A36O-08 84.000000 16.000000
## 484 TCGA-TM-A84T-01A-11D-A36O-08 60.000000 40.000000
## 485 TCGA-TQ-A7RF-01A-11D-A33T-08 62.500000 37.500000
## 486 TCGA-TQ-A7RG-01A-11D-A33T-08 79.411765 20.588235
## 487 TCGA-TQ-A7RH-01A-12D-A34A-08 76.470588 23.529412
## 488 TCGA-TQ-A7RI-01A-11D-A33T-08 78.787879 21.212121
## 489 TCGA-TQ-A7RJ-01A-11D-A33T-08 61.666667 38.333333
## 490 TCGA-TQ-A7RK-01A-11D-A33T-08 68.965517 31.034483
## 491 TCGA-TQ-A7RK-02A-11D-A36O-08 68.965517 31.034483
## 492 TCGA-TQ-A7RM-01A-11D-A33T-08 73.076923 26.923077
## 493 TCGA-TQ-A7RN-01A-11D-A33T-08 81.081081 18.918919
## 494 TCGA-TQ-A7RO-01A-11D-A33T-08 92.307692 7.692308
## 495 TCGA-TQ-A7RP-01A-21D-A34A-08 75.000000 25.000000
## 496 TCGA-TQ-A7RQ-01A-11D-A33T-08 80.555556 19.444444
## 497 TCGA-TQ-A7RR-01A-21D-A34A-08 92.105263 7.894737
## 498 TCGA-TQ-A7RS-01A-12D-A33T-08 78.947368 21.052632
## 499 TCGA-TQ-A7RU-01A-21D-A34A-08 75.675676 24.324324
## 500 TCGA-TQ-A7RV-01A-21D-A34A-08 76.923077 23.076923
## 501 TCGA-TQ-A7RV-02A-11D-A36O-08 63.333333 36.666667
## 502 TCGA-TQ-A7RW-01A-11D-A33T-08 66.153846 33.846154
## 503 TCGA-TQ-A8XE-01A-11D-A36O-08 81.818182 18.181818
## 504 TCGA-TQ-A8XE-02A-11D-A36O-08 68.571429 31.428571
## 505 TCGA-VM-A8C8-01A-11D-A36O-08 82.692308 17.307692
## 506 TCGA-VM-A8C9-01A-11D-A36O-08 75.000000 25.000000
## 507 TCGA-VM-A8CA-01A-11D-A36O-08 84.848485 15.151515
## 508 TCGA-VM-A8CB-01A-11D-A36O-08 78.125000 21.875000
## 509 TCGA-VM-A8CD-01A-11D-A36O-08 67.741935 32.258065
## 510 TCGA-VM-A8CE-01A-11D-A36O-08 59.090909 40.909091
## 511 TCGA-VM-A8CF-01A-11D-A36O-08 64.583333 35.416667
## 512 TCGA-VM-A8CH-01A-12D-A36O-08 75.000000 25.000000
## 513 TCGA-VV-A829-01A-21D-A36O-08 80.555556 19.444444
## 514 TCGA-VV-A86M-01A-11D-A36O-08 56.250000 43.750000
## 515 TCGA-VW-A7QS-01A-12D-A33T-08 78.723404 21.276596
## 516 TCGA-VW-A8FI-01A-11D-A36O-08 82.432432 17.567568
## 517 TCGA-W9-A837-01A-11D-A36O-08 75.000000 25.000000
## 518 TCGA-WH-A86K-01A-11D-A36O-08 74.509804 25.490196
## 519 TCGA-WY-A858-01A-11D-A36O-08 82.857143 17.142857
## 520 TCGA-WY-A859-01A-12D-A36O-08 52.777778 47.222222
## 521 TCGA-WY-A85A-01A-21D-A36O-08 81.250000 18.750000
## 522 TCGA-WY-A85B-01A-11D-A36O-08 76.470588 23.529412
## 523 TCGA-WY-A85C-01A-11D-A36O-08 67.647059 32.352941
## 524 TCGA-WY-A85D-01A-11D-A36O-08 71.739130 28.260870
## 525 TCGA-WY-A85E-01A-11D-A36O-08 61.445783 38.554217###3. Mutation Load Comparison Across TCGA Cohorts
# Compare mutation load with other TCGA cohorts
png(file.path(out_dir, "mutation_load_comparison.png"), width = 10, height = 8, units = "in", res = 300)
tcgaCompare(maf = lgg, cohortName = 'LGG', logscale = TRUE)## $median_mutation_burden
## Cohort Cohort_Size Median_Mutations Median_Mutations_log10
## <char> <int> <num> <num>
## 1: LAML 137 9.0 0.9542425
## 2: PCPG 183 9.0 0.9542425
## 3: THCA 499 10.0 1.0000000
## 4: UVM 80 11.5 1.0606978
## 5: TGCT 133 13.0 1.1139434
## 6: THYM 123 14.0 1.1461280
## 7: KICH 66 19.5 1.2900346
## 8: ACC 92 25.5 1.4065402
## 9: LGG 1048 27.0 1.4313638
## 10: MESO 82 27.0 1.4313638
## 11: PRAD 495 27.0 1.4313638
## 12: PAAD 176 35.0 1.5440680
## 13: BRCA 1025 40.0 1.6020600
## 14: SARC 239 40.0 1.6020600
## 15: CHOL 36 40.5 1.6074550
## 16: UCS 57 46.0 1.6627578
## 17: GBM 398 51.0 1.7075702
## 18: KIRC 370 52.0 1.7160033
## 19: KIRP 282 65.0 1.8129134
## 20: OV 411 66.0 1.8195439
## 21: UCEC 531 75.0 1.8750613
## 22: LIHC 365 82.0 1.9138139
## 23: CESC 291 86.0 1.9344985
## 24: READ 150 88.5 1.9469433
## 25: ESCA 185 103.0 2.0128372
## 26: HNSC 509 106.0 2.0253059
## 27: DLBC 37 110.0 2.0413927
## 28: STAD 438 114.5 2.0588055
## 29: COAD 406 115.0 2.0606978
## 30: BLCA 411 169.0 2.2278867
## 31: LUAD 516 198.0 2.2966652
## 32: LUSC 485 229.0 2.3598355
## 33: SKCM 468 406.5 2.6090605
## Cohort Cohort_Size Median_Mutations Median_Mutations_log10
##
## $mutation_burden_perSample
## Tumor_Sample_Barcode total cohort
## <fctr> <num> <fctr>
## 1: TCGA-AB-2808-03B-01W-0728-08 741 LAML
## 2: TCGA-AB-2828-03B-01W-0728-08 718 LAML
## 3: TCGA-AB-2826-03B-01W-0728-08 616 LAML
## 4: TCGA-AB-2806-03B-01W-0728-08 491 LAML
## 5: TCGA-AB-2833-03B-01W-0728-08 445 LAML
## ---
## 10720: TCGA-FR-A2OS-01A-11D-A21A-08 13 SKCM
## 10721: TCGA-BF-AAP8-01A-11D-A401-08 11 SKCM
## 10722: TCGA-EB-A4IQ-01A-12D-A25O-08 9 SKCM
## 10723: TCGA-EB-A4OZ-01A-12D-A25O-08 9 SKCM
## 10724: TCGA-D3-A8GE-06A-11D-A372-08 6 SKCM
##
## $pairwise_t_test
## Cohort1 Cohort2 Pval
## <char> <fctr> <num>
## 1: UCEC LGG 4.046377e-107
## 2: UCEC BRCA 2.862977e-100
## 3: UCEC THCA 2.109525e-85
## 4: UCEC PRAD 2.903998e-80
## 5: UCEC KIRC 4.842719e-67
## ---
## 524: PAAD GBM 9.945168e-01
## 525: MESO KICH 9.945168e-01
## 526: THCA TGCT 9.945168e-01
## 527: UVM TGCT 9.945168e-01
## 528: UVM THCA 9.945168e-01dev.off() ## png
## 2tcgaCompare(maf = lgg, cohortName = 'LGG', logscale = TRUE)
## $median_mutation_burden
## Cohort Cohort_Size Median_Mutations Median_Mutations_log10
## <char> <int> <num> <num>
## 1: LAML 137 9.0 0.9542425
## 2: PCPG 183 9.0 0.9542425
## 3: THCA 499 10.0 1.0000000
## 4: UVM 80 11.5 1.0606978
## 5: TGCT 133 13.0 1.1139434
## 6: THYM 123 14.0 1.1461280
## 7: KICH 66 19.5 1.2900346
## 8: ACC 92 25.5 1.4065402
## 9: LGG 1048 27.0 1.4313638
## 10: MESO 82 27.0 1.4313638
## 11: PRAD 495 27.0 1.4313638
## 12: PAAD 176 35.0 1.5440680
## 13: BRCA 1025 40.0 1.6020600
## 14: SARC 239 40.0 1.6020600
## 15: CHOL 36 40.5 1.6074550
## 16: UCS 57 46.0 1.6627578
## 17: GBM 398 51.0 1.7075702
## 18: KIRC 370 52.0 1.7160033
## 19: KIRP 282 65.0 1.8129134
## 20: OV 411 66.0 1.8195439
## 21: UCEC 531 75.0 1.8750613
## 22: LIHC 365 82.0 1.9138139
## 23: CESC 291 86.0 1.9344985
## 24: READ 150 88.5 1.9469433
## 25: ESCA 185 103.0 2.0128372
## 26: HNSC 509 106.0 2.0253059
## 27: DLBC 37 110.0 2.0413927
## 28: STAD 438 114.5 2.0588055
## 29: COAD 406 115.0 2.0606978
## 30: BLCA 411 169.0 2.2278867
## 31: LUAD 516 198.0 2.2966652
## 32: LUSC 485 229.0 2.3598355
## 33: SKCM 468 406.5 2.6090605
## Cohort Cohort_Size Median_Mutations Median_Mutations_log10
##
## $mutation_burden_perSample
## Tumor_Sample_Barcode total cohort
## <fctr> <num> <fctr>
## 1: TCGA-AB-2808-03B-01W-0728-08 741 LAML
## 2: TCGA-AB-2828-03B-01W-0728-08 718 LAML
## 3: TCGA-AB-2826-03B-01W-0728-08 616 LAML
## 4: TCGA-AB-2806-03B-01W-0728-08 491 LAML
## 5: TCGA-AB-2833-03B-01W-0728-08 445 LAML
## ---
## 10720: TCGA-FR-A2OS-01A-11D-A21A-08 13 SKCM
## 10721: TCGA-BF-AAP8-01A-11D-A401-08 11 SKCM
## 10722: TCGA-EB-A4IQ-01A-12D-A25O-08 9 SKCM
## 10723: TCGA-EB-A4OZ-01A-12D-A25O-08 9 SKCM
## 10724: TCGA-D3-A8GE-06A-11D-A372-08 6 SKCM
##
## $pairwise_t_test
## Cohort1 Cohort2 Pval
## <char> <fctr> <num>
## 1: UCEC LGG 4.046377e-107
## 2: UCEC BRCA 2.862977e-100
## 3: UCEC THCA 2.109525e-85
## 4: UCEC PRAD 2.903998e-80
## 5: UCEC KIRC 4.842719e-67
## ---
## 524: PAAD GBM 9.945168e-01
## 525: MESO KICH 9.945168e-01
## 526: THCA TGCT 9.945168e-01
## 527: UVM TGCT 9.945168e-01
## 528: UVM THCA 9.945168e-01Genomic Data Analysis Assessment Answers
Q1: How many positions are found in the region 1:1105411-44137860?
A: 69
Q2: How many samples are included in the VCF file?
A: 90
Q3: How many positions are there total in the VCF file?
A: 3489
Q4: How many positions have AC=1?
A: 1075
Q5: What is the ts/tv ratio?
A: 3.47
Q6: What is the median number of variants per sample in the LGG dataset?
A: 28
Session Information
sessionInfo()## R version 4.4.1 (2024-06-14 ucrt)
## Platform: x86_64-w64-mingw32/x64
## Running under: Windows 11 x64 (build 22631)
##
## Matrix products: default
##
##
## locale:
## [1] LC_COLLATE=English_United States.utf8
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] maftools_2.20.0
##
## loaded via a namespace (and not attached):
## [1] vctrs_0.6.5 cli_3.6.3 knitr_1.48
## [4] rlang_1.1.4 xfun_0.46 highr_0.11
## [7] jsonlite_1.8.9 data.table_1.16.0 htmltools_0.5.8.1
## [10] sass_0.4.9 rmarkdown_2.28 grid_4.4.1
## [13] evaluate_1.0.0 jquerylib_0.1.4 fastmap_1.2.0
## [16] yaml_2.3.10 lifecycle_1.0.4 BiocManager_1.30.25
## [19] DNAcopy_1.78.0 compiler_4.4.1 RColorBrewer_1.1-3
## [22] rstudioapi_0.16.0 R.oo_1.26.0 R.utils_2.12.3
## [25] lattice_0.22-6 digest_0.6.36 R6_2.5.1
## [28] splines_4.4.1 R.methodsS3_1.8.2 bslib_0.8.0
## [31] Matrix_1.7-0 tools_4.4.1 survival_3.7-0
## [34] cachem_1.1.0