Peds Only AML_2022
2022-11-06
## -Reading
## -Validating
## -Silent variants: 475
## -Summarizing
## -Processing clinical data
## -Finished in 0.408s elapsed (0.385s cpu)import data
## Data Frame Summary
## AML
## Dimensions: 54 x 33
## Duplicates: 0
##
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | Variable | Stats / Values | Freqs (% of Valid) |
## +==============================================================================================+===========================+====================+
## | number | Mean (sd) : 27 (15.44) | 53 distinct values |
## | [numeric] | min < med < max: | |
## | | 1 < 27 < 53 | |
## | | IQR (CV) : 26 (0.57) | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | gender | 1. Female | 19 (35.8%) |
## | [character] | 2. Male | 34 (64.2%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | age_at_diagnosis | Mean (sd) : 9.31 (5.52) | 53 distinct values |
## | [numeric] | min < med < max: | |
## | | 0.15 < 8.89 < 17.98 | |
## | | IQR (CV) : 9.27 (0.59) | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | fab_classfication | 1. AML/MDS | 3 ( 5.7%) |
## | [character] | 2. M0 | 6 (11.3%) |
## | | 3. M1 | 1 ( 1.9%) |
## | | 4. M2 | 19 (35.8%) |
## | | 5. M3 | 5 ( 9.4%) |
## | | 6. M4 | 10 (18.9%) |
## | | 7. M5 | 2 ( 3.8%) |
## | | 8. M7 | 4 ( 7.5%) |
## | | 9. MDS | 1 ( 1.9%) |
## | | 10. Myeloid Sarcoma | 1 ( 1.9%) |
## | | 11. NOS | 1 ( 1.9%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | aml_denovo | 1. De novo AML | 51 (96.2%) |
## | [character] | 2. MDS | 1 ( 1.9%) |
## | | 3. Therapy Related AML | 1 ( 1.9%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | sample_type | 1. Bone Marrow | 38 (73.1%) |
## | [character] | 2. Peripheral Blood | 13 (25.0%) |
## | | 3. Skin biopsy | 1 ( 1.9%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | blast_percent_in_flowcytomtry_at_time_of_ngs | Mean (sd) : 0.53 (0.24) | 19 distinct values |
## | [numeric] | min < med < max: | |
## | | 0.06 < 0.5 < 0.95 | |
## | | IQR (CV) : 0.32 (0.45) | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | blast_percent_in_bm_at_time_of_ngs | Mean (sd) : 0.97 (0.12) | 3 distinct values |
## | [numeric] | min < med < max: | |
## | | 0.5 < 1 < 1 | |
## | | IQR (CV) : 0 (0.13) | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | cbfb_gene_rearrangement | 1 distinct value | 1 : 5 (100.0%) |
## | [numeric] | | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | runx1t1_runx1_rearrangement | 1 distinct value | 1 : 8 (100.0%) |
## | [numeric] | | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | pml_rara_gene_rearrangement | 1 distinct value | 1 : 5 (100.0%) |
## | [numeric] | | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | mll_gene_rearrangement | 1 distinct value | 1 : 5 (100.0%) |
## | [numeric] | | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | x5q_or_7q | 1 distinct value | 1 : 5 (100.0%) |
## | [numeric] | | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | cytogenetic_subgroup | 1. Favorable prognosis | 19 (36.5%) |
## | [character] | 2. Normal | 5 ( 9.6%) |
## | | 3. Not applicable | 1 ( 1.9%) |
## | | 4. Poor prognosis | 19 (36.5%) |
## | | 5. Uncertain significan | 8 (15.4%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | eln_risk_group | 1. adverse | 20 (38.5%) |
## | [character] | 2. favourable | 18 (34.6%) |
## | | 3. Intermediate | 14 (26.9%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | fish | 1. Negative | 21 (39.6%) |
## | [character] | 2. RUNX1T1/RUNX1 rearra | 8 (15.1%) |
## | | 3. CBFB gene rearrangem | 5 ( 9.4%) |
## | | 4. MLL gene rearrangeme | 5 ( 9.4%) |
## | | 5. PML/RARA gene rearra | 5 ( 9.4%) |
## | | 6. Monosomy 7 | 2 ( 3.8%) |
## | | 7. Not done | 2 ( 3.8%) |
## | | 8. 5q del, 7q del | 1 ( 1.9%) |
## | | 9. 5q deletion | 1 ( 1.9%) |
## | | 10. Monosomy 16 | 1 ( 1.9%) |
## | | [ 2 others ] | 2 ( 3.8%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | cytogenetics | 1. negative | 9 (17.0%) |
## | [character] | 2. 46,XY,Inv(16)(P13.1q | 3 ( 5.7%) |
## | | 3. 46,Xy,t(8;21)(q22;q2 | 3 ( 5.7%) |
## | | 4. 46 XX, t(9;11) | 2 ( 3.8%) |
## | | 5. 46,XX,t(15;17)(q24;q | 2 ( 3.8%) |
## | | 6. 46,XY,t(6;7)(p25;q11 | 2 ( 3.8%) |
## | | 7. 45XY, -7, t(12;14) | 1 ( 1.9%) |
## | | 8. 46 XX, del(11), t(4; | 1 ( 1.9%) |
## | | 9. 46 XX,t(1;5) | 1 ( 1.9%) |
## | | 10. 46 xy t(15;17) | 1 ( 1.9%) |
## | | [ 28 others ] | 28 (52.8%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | flt3_by_pcr | 1. Negative | 40 (75.5%) |
## | [character] | 2. Not done | 2 ( 3.8%) |
## | | 3. Positive | 11 (20.8%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | flt3_tkd_itd_by_pcr | 1. FLT3- ITD | 10 (30.3%) |
## | [character] | 2. FLT3- TKD | 1 ( 3.0%) |
## | | 3. neg | 3 ( 9.1%) |
## | | 4. nega | 1 ( 3.0%) |
## | | 5. negat | 2 ( 6.1%) |
## | | 6. Negatice | 2 ( 6.1%) |
## | | 7. negative | 14 (42.4%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | variant_type_vus_pathogenic | 1. Negative | 9 (16.7%) |
## | [character] | 2. Pathogenic | 37 (68.5%) |
## | | 3. VUS | 8 (14.8%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | pathogenic_vus_gene | 1. KIT | 7 (15.6%) |
## | [character] | 2. FLT3 | 6 (13.3%) |
## | | 3. NRAS | 5 (11.1%) |
## | | 4. GATA2 | 4 ( 8.9%) |
## | | 5. KRAS | 4 ( 8.9%) |
## | | 6. EZH2 | 2 ( 4.4%) |
## | | 7. NPM1 | 2 ( 4.4%) |
## | | 8. ZRSR2 | 2 ( 4.4%) |
## | | 9. ASXL1 | 1 ( 2.2%) |
## | | 10. BCORL1 | 1 ( 2.2%) |
## | | [ 11 others ] | 11 (24.4%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | alternate_variant_frequency_pathogenic_vus | Mean (sd) : 0.34 (0.19) | 33 distinct values |
## | [numeric] | min < med < max: | |
## | | 0.01 < 0.36 < 0.9 | |
## | | IQR (CV) : 0.27 (0.55) | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | disease_status_cr1_non_remission_others | 1. CR1 | 33 (62.3%) |
## | [character] | 2. CR2 | 1 ( 1.9%) |
## | | 3. Induction death | 2 ( 3.8%) |
## | | 4. Non-Remission | 17 (32.1%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | event_yes_no | 1. No | 33 (62.3%) |
## | [character] | 2. Yes | 20 (37.7%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | event | Min : 0 | 0 : 33 (62.3%) |
## | [numeric] | Mean : 0.38 | 1 : 20 (37.7%) |
## | | Max : 1 | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | efs | Mean (sd) : 23.02 (15.67) | 52 distinct values |
## | [numeric] | min < med < max: | |
## | | 0.1 < 19.47 < 53.97 | |
## | | IQR (CV) : 26.73 (0.68) | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | type_of_1st_event_relapse_refractory_death | 1. Death | 2 (10.0%) |
## | [character] | 2. Refractory | 4 (20.0%) |
## | | 3. Relapse | 14 (70.0%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | type_of_2nd_event_relapse_refractory_death | 1. Death | 15 (100.0%) |
## | [character] | | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | status_at_last_follow_up_alive_dead | 1. Alive | 38 (71.7%) |
## | [character] | 2. Dead | 15 (28.3%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | dead | Min : 0 | 0 : 38 (71.7%) |
## | [numeric] | Mean : 0.28 | 1 : 15 (28.3%) |
## | | Max : 1 | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | os | Mean (sd) : 26.1 (14.59) | 52 distinct values |
## | [numeric] | min < med < max: | |
## | | 0.1 < 24.63 < 53.97 | |
## | | IQR (CV) : 23.97 (0.56) | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | when_ngs_was_done_in_deno_novo_aml_at_diagnosis_or_in_cr_in_relapsed_aml_at_relapse_or_in_cr | 1. At Diagnosis of deno | 53 (100.0%) |
## | [character] | | |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+
## | Tumor_Sample_Barcode | 1. 116365 | 1 ( 1.9%) |
## | [character] | 2. 150388 | 1 ( 1.9%) |
## | | 3. 150408 | 1 ( 1.9%) |
## | | 4. 150522 | 1 ( 1.9%) |
## | | 5. 151811 | 1 ( 1.9%) |
## | | 6. 151858 | 1 ( 1.9%) |
## | | 7. 155821 | 1 ( 1.9%) |
## | | 8. 157510 | 1 ( 1.9%) |
## | | 9. 158732 | 1 ( 1.9%) |
## | | 10. 159596 | 1 ( 1.9%) |
## | | [ 43 others ] | 43 (81.1%) |
## +----------------------------------------------------------------------------------------------+---------------------------+--------------------+MAF file
patient chch
## -Validating
## --Removed 33 duplicated variants
## -Silent variants: 4
## -Summarizing
## -Processing clinical data
## -Finished in 0.082s elapsed (0.066s cpu)Summary of all VCF present
## An object of class MAF
## ID summary Mean Median
## 1: NCBI_Build GRCh37 NA NA
## 2: Center . NA NA
## 3: Samples 43 NA NA
## 4: nGenes 34 NA NA
## 5: Frame_Shift_Del 12 0.279 0
## 6: Frame_Shift_Ins 4 0.093 0
## 7: Missense_Mutation 109 2.535 2
## 8: Nonsense_Mutation 4 0.093 0
## 9: Splice_Site 4 0.093 0
## 10: total 133 3.093 2
## Frequencies
## MAFdata$Variant_Classification
## Type: Factor
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ----------------------- ------ --------- -------------- --------- --------------
## Missense_Mutation 109 81.95 81.95 81.95 81.95
## Frame_Shift_Del 12 9.02 90.98 9.02 90.98
## Frame_Shift_Ins 4 3.01 93.98 3.01 93.98
## Nonsense_Mutation 4 3.01 96.99 3.01 96.99
## Splice_Site 4 3.01 100.00 3.01 100.00
## <NA> 0 0.00 100.00
## Total 133 100.00 100.00 100.00 100.00## Frequencies
## MAFdata$Hugo_Symbol
## Type: Character
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ------------ ------ --------- -------------- --------- --------------
## KRAS 16 12.03 12.03 12.03 12.03
## TP53 15 11.28 23.31 11.28 23.31
## NRAS 13 9.77 33.08 9.77 33.08
## PTPN11 13 9.77 42.86 9.77 42.86
## PTEN 9 6.77 49.62 6.77 49.62
## CDKN2A 7 5.26 54.89 5.26 54.89
## GATA2 7 5.26 60.15 5.26 60.15
## KIT 6 4.51 64.66 4.51 64.66
## CEBPA 5 3.76 68.42 3.76 68.42
## CBL 4 3.01 71.43 3.01 71.43
## DNMT3A 4 3.01 74.44 3.01 74.44
## WT1 3 2.26 76.69 2.26 76.69
## FLT3 2 1.50 78.20 1.50 78.20
## IDH2 2 1.50 79.70 1.50 79.70
## KDM6A 2 1.50 81.20 1.50 81.20
## KMT2A 2 1.50 82.71 1.50 82.71
## NOTCH1 2 1.50 84.21 1.50 84.21
## NPM1 2 1.50 85.71 1.50 85.71
## SETBP1 2 1.50 87.22 1.50 87.22
## SF3B1 2 1.50 88.72 1.50 88.72
## SMC1A 2 1.50 90.23 1.50 90.23
## ABL1 1 0.75 90.98 0.75 90.98
## ATRX 1 0.75 91.73 0.75 91.73
## BCOR 1 0.75 92.48 0.75 92.48
## FBXW7 1 0.75 93.23 0.75 93.23
## IDH1 1 0.75 93.98 0.75 93.98
## IKZF1 1 0.75 94.74 0.75 94.74
## JAK2 1 0.75 95.49 0.75 95.49
## MPL 1 0.75 96.24 0.75 96.24
## MYD88 1 0.75 96.99 0.75 96.99
## PDGFRA 1 0.75 97.74 0.75 97.74
## RAD21 1 0.75 98.50 0.75 98.50
## RUNX1 1 0.75 99.25 0.75 99.25
## U2AF1 1 0.75 100.00 0.75 100.00
## <NA> 0 0.00 100.00
## Total 133 100.00 100.00 100.00 100.00## Frequencies
## MAFdata$SIFT
## Type: Character
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## -------------------------------------- ------ --------- -------------- --------- --------------
## deleterious(0) 62 46.62 46.62 46.62 46.62
## (Empty string) 24 18.05 64.66 18.05 64.66
## deleterious(0.01) 8 6.02 70.68 6.02 70.68
## deleterious(0.02) 7 5.26 75.94 5.26 75.94
## deleterious(0.03) 5 3.76 79.70 3.76 79.70
## deleterious_low_confidence(0) 4 3.01 82.71 3.01 82.71
## tolerated(0.06) 4 3.01 85.71 3.01 85.71
## deleterious(0.05) 3 2.26 87.97 2.26 87.97
## tolerated(0.09) 3 2.26 90.23 2.26 90.23
## deleterious_low_confidence(0.01) 2 1.50 91.73 1.50 91.73
## deleterious(0.04) 2 1.50 93.23 1.50 93.23
## tolerated(0.05) 1 0.75 93.98 0.75 93.98
## tolerated(0.08) 1 0.75 94.74 0.75 94.74
## tolerated(0.1) 1 0.75 95.49 0.75 95.49
## tolerated(0.12) 1 0.75 96.24 0.75 96.24
## tolerated(0.14) 1 0.75 96.99 0.75 96.99
## tolerated(0.19) 1 0.75 97.74 0.75 97.74
## tolerated(0.21) 1 0.75 98.50 0.75 98.50
## tolerated(0.28) 1 0.75 99.25 0.75 99.25
## tolerated(0.52) 1 0.75 100.00 0.75 100.00
## <NA> 0 0.00 100.00
## Total 133 100.00 100.00 100.00 100.00## Frequencies
## MAFdata$polyphen_summary
## Type: Character
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ----------------------- ------ --------- -------------- --------- --------------
## probably_damaging 58 43.61 43.61 43.61 43.61
## benign 38 28.57 72.18 28.57 72.18
## (Empty string) 24 18.05 90.23 18.05 90.23
## possibly_damaging 13 9.77 100.00 9.77 100.00
## <NA> 0 0.00 100.00
## Total 133 100.00 100.00 100.00 100.00## Frequencies
## MAFdata$CLIN_SIG
## Type: Character
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ------------------------------------------------------------------------------------------------------ ------ --------- -------------- --------- --------------
## pathogenic 47 36.15 36.15 36.15 36.15
## pathogenic,likely_pathogenic 26 20.00 56.15 20.00 56.15
## likely_pathogenic 21 16.15 72.31 16.15 72.31
## likely_pathogenic,pathogenic 14 10.77 83.08 10.77 83.08
## conflicting_interpretations_of_pathogenicity,uncertain_significance 3 2.31 85.38 2.31 85.38
## conflicting_interpretations_of_pathogenicity,likely_pathogenic,uncertain_significance 2 1.54 86.92 1.54 86.92
## other,likely_pathogenic,pathogenic 2 1.54 88.46 1.54 88.46
## uncertain_significance,likely_pathogenic 2 1.54 90.00 1.54 90.00
## uncertain_significance,pathogenic 2 1.54 91.54 1.54 91.54
## conflicting_interpretations_of_pathogenicity,likely_pathogenic 1 0.77 92.31 0.77 92.31
## likely_pathogenic,other 1 0.77 93.08 0.77 93.08
## likely_pathogenic,pathogenic/likely_pathogenic 1 0.77 93.85 0.77 93.85
## likely_pathogenic,uncertain_significance 1 0.77 94.62 0.77 94.62
## not_provided,pathogenic 1 0.77 95.38 0.77 95.38
## pathogenic,likely_pathogenic,not_provided 1 0.77 96.15 0.77 96.15
## pathogenic,likely_pathogenic,uncertain_significance,conflicting_interpretations_of_pathogenicity 1 0.77 96.92 0.77 96.92
## pathogenic,not_provided,likely_pathogenic 1 0.77 97.69 0.77 97.69
## risk_factor,likely_pathogenic 1 0.77 98.46 0.77 98.46
## uncertain_significance,likely_pathogenic,pathogenic 1 0.77 99.23 0.77 99.23
## uncertain_significance,pathogenic,likely_pathogenic 1 0.77 100.00 0.77 100.00
## <NA> 0 0.00 100.00
## Total 130 100.00 100.00 100.00 100.00
## # A tibble: 21 × 2
## pathogenic_vus_gene n
## <chr> <int>
## 1 KIT 7
## 2 FLT3 6
## 3 NRAS 5
## 4 GATA2 4
## 5 KRAS 4
## 6 EZH2 2
## 7 NPM1 2
## 8 ZRSR2 2
## 9 ASXL1 1
## 10 BCORL1 1
## # … with 11 more rows
## # ℹ Use `print(n = ...)` to see more rowsSummary of PEDIATRIC mutations
## Frequencies
## MAFdata$Variant_Classification
## Type: Factor
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ----------------------- ------ --------- -------------- --------- --------------
## Missense_Mutation 109 81.95 81.95 81.95 81.95
## Frame_Shift_Del 12 9.02 90.98 9.02 90.98
## Frame_Shift_Ins 4 3.01 93.98 3.01 93.98
## Nonsense_Mutation 4 3.01 96.99 3.01 96.99
## Splice_Site 4 3.01 100.00 3.01 100.00
## <NA> 0 0.00 100.00
## Total 133 100.00 100.00 100.00 100.00## Frequencies
## MAFdata$Hugo_Symbol
## Type: Character
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ------------ ------ --------- -------------- --------- --------------
## KRAS 16 12.03 12.03 12.03 12.03
## TP53 15 11.28 23.31 11.28 23.31
## NRAS 13 9.77 33.08 9.77 33.08
## PTPN11 13 9.77 42.86 9.77 42.86
## PTEN 9 6.77 49.62 6.77 49.62
## CDKN2A 7 5.26 54.89 5.26 54.89
## GATA2 7 5.26 60.15 5.26 60.15
## KIT 6 4.51 64.66 4.51 64.66
## CEBPA 5 3.76 68.42 3.76 68.42
## CBL 4 3.01 71.43 3.01 71.43
## DNMT3A 4 3.01 74.44 3.01 74.44
## WT1 3 2.26 76.69 2.26 76.69
## FLT3 2 1.50 78.20 1.50 78.20
## IDH2 2 1.50 79.70 1.50 79.70
## KDM6A 2 1.50 81.20 1.50 81.20
## KMT2A 2 1.50 82.71 1.50 82.71
## NOTCH1 2 1.50 84.21 1.50 84.21
## NPM1 2 1.50 85.71 1.50 85.71
## SETBP1 2 1.50 87.22 1.50 87.22
## SF3B1 2 1.50 88.72 1.50 88.72
## SMC1A 2 1.50 90.23 1.50 90.23
## ABL1 1 0.75 90.98 0.75 90.98
## ATRX 1 0.75 91.73 0.75 91.73
## BCOR 1 0.75 92.48 0.75 92.48
## FBXW7 1 0.75 93.23 0.75 93.23
## IDH1 1 0.75 93.98 0.75 93.98
## IKZF1 1 0.75 94.74 0.75 94.74
## JAK2 1 0.75 95.49 0.75 95.49
## MPL 1 0.75 96.24 0.75 96.24
## MYD88 1 0.75 96.99 0.75 96.99
## PDGFRA 1 0.75 97.74 0.75 97.74
## RAD21 1 0.75 98.50 0.75 98.50
## RUNX1 1 0.75 99.25 0.75 99.25
## U2AF1 1 0.75 100.00 0.75 100.00
## <NA> 0 0.00 100.00
## Total 133 100.00 100.00 100.00 100.00## Frequencies
## MAFdata$SIFT
## Type: Character
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## -------------------------------------- ------ --------- -------------- --------- --------------
## deleterious(0) 62 46.62 46.62 46.62 46.62
## (Empty string) 24 18.05 64.66 18.05 64.66
## deleterious(0.01) 8 6.02 70.68 6.02 70.68
## deleterious(0.02) 7 5.26 75.94 5.26 75.94
## deleterious(0.03) 5 3.76 79.70 3.76 79.70
## deleterious_low_confidence(0) 4 3.01 82.71 3.01 82.71
## tolerated(0.06) 4 3.01 85.71 3.01 85.71
## deleterious(0.05) 3 2.26 87.97 2.26 87.97
## tolerated(0.09) 3 2.26 90.23 2.26 90.23
## deleterious_low_confidence(0.01) 2 1.50 91.73 1.50 91.73
## deleterious(0.04) 2 1.50 93.23 1.50 93.23
## tolerated(0.05) 1 0.75 93.98 0.75 93.98
## tolerated(0.08) 1 0.75 94.74 0.75 94.74
## tolerated(0.1) 1 0.75 95.49 0.75 95.49
## tolerated(0.12) 1 0.75 96.24 0.75 96.24
## tolerated(0.14) 1 0.75 96.99 0.75 96.99
## tolerated(0.19) 1 0.75 97.74 0.75 97.74
## tolerated(0.21) 1 0.75 98.50 0.75 98.50
## tolerated(0.28) 1 0.75 99.25 0.75 99.25
## tolerated(0.52) 1 0.75 100.00 0.75 100.00
## <NA> 0 0.00 100.00
## Total 133 100.00 100.00 100.00 100.00## Frequencies
## MAFdata$polyphen_summary
## Type: Character
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ----------------------- ------ --------- -------------- --------- --------------
## probably_damaging 58 43.61 43.61 43.61 43.61
## benign 38 28.57 72.18 28.57 72.18
## (Empty string) 24 18.05 90.23 18.05 90.23
## possibly_damaging 13 9.77 100.00 9.77 100.00
## <NA> 0 0.00 100.00
## Total 133 100.00 100.00 100.00 100.00## Frequencies
## MAFdata$CLIN_SIG
## Type: Character
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ------------------------------------------------------------------------------------------------------ ------ --------- -------------- --------- --------------
## pathogenic 47 36.15 36.15 36.15 36.15
## pathogenic,likely_pathogenic 26 20.00 56.15 20.00 56.15
## likely_pathogenic 21 16.15 72.31 16.15 72.31
## likely_pathogenic,pathogenic 14 10.77 83.08 10.77 83.08
## conflicting_interpretations_of_pathogenicity,uncertain_significance 3 2.31 85.38 2.31 85.38
## conflicting_interpretations_of_pathogenicity,likely_pathogenic,uncertain_significance 2 1.54 86.92 1.54 86.92
## other,likely_pathogenic,pathogenic 2 1.54 88.46 1.54 88.46
## uncertain_significance,likely_pathogenic 2 1.54 90.00 1.54 90.00
## uncertain_significance,pathogenic 2 1.54 91.54 1.54 91.54
## conflicting_interpretations_of_pathogenicity,likely_pathogenic 1 0.77 92.31 0.77 92.31
## likely_pathogenic,other 1 0.77 93.08 0.77 93.08
## likely_pathogenic,pathogenic/likely_pathogenic 1 0.77 93.85 0.77 93.85
## likely_pathogenic,uncertain_significance 1 0.77 94.62 0.77 94.62
## not_provided,pathogenic 1 0.77 95.38 0.77 95.38
## pathogenic,likely_pathogenic,not_provided 1 0.77 96.15 0.77 96.15
## pathogenic,likely_pathogenic,uncertain_significance,conflicting_interpretations_of_pathogenicity 1 0.77 96.92 0.77 96.92
## pathogenic,not_provided,likely_pathogenic 1 0.77 97.69 0.77 97.69
## risk_factor,likely_pathogenic 1 0.77 98.46 0.77 98.46
## uncertain_significance,likely_pathogenic,pathogenic 1 0.77 99.23 0.77 99.23
## uncertain_significance,pathogenic,likely_pathogenic 1 0.77 100.00 0.77 100.00
## <NA> 0 0.00 100.00
## Total 130 100.00 100.00 100.00 100.00lollipops
plot variant allele frquency
## [1] "Pediatric"
# survival ## according to mutations in 10 top mutated genes
x5q_or_7q 1 0 (NaN) 4 (100.0) mll_gene_rearrangement 1 0 (NaN) 5 (100.0) runx1t1_runx1_rearrangement 1 0 (NaN) 5 (100.0) cbfb_gene_rearrangement 1 0 (NaN) 4 (100.0) pml_rara_gene_rearrangement
survival curves for all patients
#pediatrics
## gene1 gene2 pValue oddsRatio 00 11 01 10 pAdj
## 1: KMT2A KDM6A 0.001107420 Inf 41 2 0 0 0.03009293
## 2: KDM6A CBL 0.006644518 Inf 39 2 2 0 0.15380829
## 3: KMT2A CBL 0.006644518 Inf 39 2 2 0 0.15380829
## 4: SF3B1 KIT 0.016611296 Inf 37 2 4 0 0.31460787
## 5: SF3B1 PTEN 0.016611296 Inf 37 2 4 0 0.31460787
## ---
## 296: NOTCH1 WT1 1.000000000 0 38 0 3 2 1.00000000
## 297: NPM1 WT1 1.000000000 0 38 0 3 2 1.00000000
## 298: SETBP1 WT1 1.000000000 0 38 0 3 2 1.00000000
## 299: SF3B1 WT1 1.000000000 0 38 0 3 2 1.00000000
## 300: SMC1A WT1 1.000000000 0 38 0 3 2 1.00000000
## Event pair event_ratio
## 1: Co_Occurence KDM6A, KMT2A 2/0
## 2: Co_Occurence CBL, KDM6A 2/2
## 3: Co_Occurence CBL, KMT2A 2/2
## 4: Co_Occurence KIT, SF3B1 2/4
## 5: Co_Occurence PTEN, SF3B1 2/4
## ---
## 296: Mutually_Exclusive NOTCH1, WT1 0/5
## 297: Mutually_Exclusive NPM1, WT1 0/5
## 298: Mutually_Exclusive SETBP1, WT1 0/5
## 299: Mutually_Exclusive SF3B1, WT1 0/5
## 300: Mutually_Exclusive SMC1A, WT1 0/5## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
## LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3
##
## locale:
## [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
## [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
## [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] broom_1.0.0 cmprsk_2.2-11 forcats_0.5.1 purrr_0.3.4
## [5] readr_2.1.2 tibble_3.1.7 tidyverse_1.3.2 BBmisc_1.12
## [9] maftools_2.12.0 plotly_4.10.0 gtsummary_1.6.1 here_1.0.1
## [13] readxl_1.4.0 gt_0.6.0 Hmisc_4.7-0 Formula_1.2-4
## [17] lattice_0.20-45 finalfit_1.0.4 tidyr_1.2.0 lubridate_1.8.0
## [21] stringr_1.4.0 dplyr_1.0.9 survminer_0.4.9 ggpubr_0.4.0
## [25] ggplot2_3.3.6 survival_3.3-1 summarytools_1.0.1
##
## loaded via a namespace (and not attached):
## [1] backports_1.4.1 plyr_1.8.7 lazyeval_0.2.2
## [4] splines_4.2.1 pryr_0.1.5 digest_0.6.29
## [7] htmltools_0.5.3 magick_2.7.3 fansi_1.0.3
## [10] magrittr_2.0.3 checkmate_2.1.0 googlesheets4_1.0.0
## [13] cluster_2.1.3 tzdb_0.3.0 modelr_0.1.8
## [16] matrixStats_0.62.0 R.utils_2.12.0 jpeg_0.1-9
## [19] colorspace_2.0-3 rvest_1.0.2 haven_2.5.0
## [22] xfun_0.31 tcltk_4.2.1 crayon_1.5.1
## [25] jsonlite_1.8.0 zoo_1.8-10 glue_1.6.2
## [28] gtable_0.3.0 gargle_1.2.0 car_3.1-0
## [31] abind_1.4-5 rapportools_1.1 scales_1.2.0
## [34] DBI_1.1.3 rstatix_0.7.0 Rcpp_1.0.9
## [37] viridisLite_0.4.0 xtable_1.8-4 htmlTable_2.4.1
## [40] foreign_0.8-82 km.ci_0.5-6 htmlwidgets_1.5.4
## [43] httr_1.4.3 RColorBrewer_1.1-3 ellipsis_0.3.2
## [46] mice_3.14.0 pkgconfig_2.0.3 R.methodsS3_1.8.2
## [49] nnet_7.3-17 sass_0.4.2 dbplyr_2.2.1
## [52] deldir_1.0-6 utf8_1.2.2 janitor_2.1.0
## [55] DNAcopy_1.70.0 tidyselect_1.1.2 rlang_1.0.4
## [58] reshape2_1.4.4 munsell_0.5.0 cellranger_1.1.0
## [61] tools_4.2.1 cachem_1.0.6 cli_3.3.0
## [64] generics_0.1.3 evaluate_0.15 fastmap_1.1.0
## [67] yaml_2.3.5 knitr_1.39 fs_1.5.2
## [70] pander_0.6.5 survMisc_0.5.6 R.oo_1.25.0
## [73] xml2_1.3.3 compiler_4.2.1 rstudioapi_0.13
## [76] png_0.1-7 ggsignif_0.6.3 reprex_2.0.1
## [79] broom.helpers_1.8.0 bslib_0.4.0 stringi_1.7.8
## [82] highr_0.9 Matrix_1.4-1 KMsurv_0.1-5
## [85] vctrs_0.4.1 pillar_1.8.0 lifecycle_1.0.1
## [88] jquerylib_0.1.4 data.table_1.14.2 R6_2.5.1
## [91] latticeExtra_0.6-30 gridExtra_2.3 codetools_0.2-18
## [94] boot_1.3-28 MASS_7.3-57 assertthat_0.2.1
## [97] rprojroot_2.0.3 withr_2.5.0 hms_1.1.1
## [100] grid_4.2.1 rpart_4.1.16 rmarkdown_2.14
## [103] snakecase_0.11.0 carData_3.0-5 googledrive_2.0.0
## [106] base64enc_0.1-3 interp_1.1-3