Data
## [1] "genome.wustl.edu_CESC.IlluminaGA_DNASeq_curated.Level_2.1.0.0.somatic.maf"
## [2] "genome.wustl.edu_CESC.IlluminaHiSeq_DNASeq_automated.1.3.0.somatic.maf"
## [3] "ucsc.edu_CESC.IlluminaGA_DNASeq_automated.Level_2.1.1.0.somatic.maf"
## [4] "bcgsc.ca_CESC.IlluminaHiSeq_DNASeq.1.somatic.maf"
## [5] "PR_TCGA_CESC_PAIR_Capture_All_Pairs.aggregated.capture.tcga.uuid.somatic.maf"
## [6] "gsc_CESC_pairs.aggregated.capture.tcga.uuid.automated.somatic.maf"
## $genome.wustl.edu_CESC.IlluminaGA_DNASeq_curated.Level_2.1.0.0.somatic.maf
## # A tibble: 46,547 x 66
## Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position
## <chr> <int> <chr> <dbl> <chr> <int>
## 1 A1BG 1 genom… 37 19 58864353
## 2 A1BG-AS1 503538 genom… 37 19 58864179
## 3 A1CF 29974 genom… 37 10 52587925
## 4 A1CF 29974 genom… 37 10 52601652
## 5 A2M 2 genom… 37 12 9262517
## 6 A2M 2 genom… 37 12 9265031
## 7 A2M 2 genom… 37 12 9265042
## 8 A2ML1 144568 genom… 37 12 8982339
## 9 A2ML1 144568 genom… 37 12 8997932
## 10 A2ML1 144568 genom… 37 12 9013793
## # … with 46,537 more rows, and 60 more variables: End_Position <int>,
## # Strand <chr>, Variant_Classification <chr>, Variant_Type <chr>,
## # Reference_Allele <chr>, Tumor_Seq_Allele1 <chr>, Tumor_Seq_Allele2 <chr>,
## # dbSNP_RS <lgl>, dbSNP_Val_Status <lgl>, Tumor_Sample_Barcode <chr>,
## # Matched_Norm_Sample_Barcode <chr>, Match_Norm_Seq_Allele1 <chr>,
## # Match_Norm_Seq_Allele2 <chr>, Tumor_Validation_Allele1 <lgl>,
## # Tumor_Validation_Allele2 <lgl>, Match_Norm_Validation_Allele1 <lgl>,
## # Match_Norm_Validation_Allele2 <lgl>, Verification_Status <chr>,
## # Validation_Status <chr>, Mutation_Status <chr>, Sequencing_Phase <chr>,
## # Sequence_Source <chr>, Validation_Method <chr>, Score <lgl>,
## # BAM_File <lgl>, Sequencer <chr>, Tumor_Sample_UUID <chr>,
## # Matched_Norm_Sample_UUID <chr>, chromosome_name <chr>, start <dbl>,
## # stop <dbl>, reference <chr>, variant <chr>, type <chr>, gene_name <chr>,
## # transcript_name <chr>, transcript_species <chr>, transcript_source <chr>,
## # transcript_version <chr>, strand <dbl>, transcript_status <chr>,
## # trv_type <chr>, c_position <chr>, amino_acid_change <chr>, ucsc_cons <chr>,
## # domain <chr>, all_domains <chr>, deletion_substructures <chr>,
## # transcript_error <chr>, default_gene_name <chr>, gene_name_source <chr>,
## # gene_name_source_1 <chr>, tumor_ref_reads <dbl>, tumor_var_reads <dbl>,
## # tumor_vaf <dbl>, normal_ref_reads <dbl>, normal_var_reads <dbl>,
## # normal_vaf <dbl>, dbSNP_rsID <chr>, GMAF <chr>
##
## $genome.wustl.edu_CESC.IlluminaHiSeq_DNASeq_automated.1.3.0.somatic.maf
## # A tibble: 38,693 x 73
## Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position
## <chr> <int> <chr> <dbl> <chr> <int>
## 1 A1BG 0 genom… 37 19 58864353
## 2 A1BG-AS1 0 genom… 37 19 58864179
## 3 A1CF 0 genom… 37 10 52587925
## 4 A1CF 0 genom… 37 10 52601652
## 5 A2M 0 genom… 37 12 9262517
## 6 A2M 0 genom… 37 12 9265031
## 7 A2M 0 genom… 37 12 9265042
## 8 A2ML1 0 genom… 37 12 8997932
## 9 A4GNT 0 genom… 37 3 137843671
## 10 AACSP1 0 genom… 37 5 178203190
## # … with 38,683 more rows, and 67 more variables: End_Position <int>,
## # Strand <chr>, Variant_Classification <chr>, Variant_Type <chr>,
## # Reference_Allele <chr>, Tumor_Seq_Allele1 <chr>, Tumor_Seq_Allele2 <chr>,
## # dbSNP_RS <lgl>, dbSNP_Val_Status <lgl>, Tumor_Sample_Barcode <chr>,
## # Matched_Norm_Sample_Barcode <chr>, Match_Norm_Seq_Allele1 <chr>,
## # Match_Norm_Seq_Allele2 <chr>, Tumor_Validation_Allele1 <chr>,
## # Tumor_Validation_Allele2 <chr>, Match_Norm_Validation_Allele1 <chr>,
## # Match_Norm_Validation_Allele2 <chr>, Verification_Status <chr>,
## # Validation_Status <chr>, Mutation_Status <chr>, Sequencing_Phase <chr>,
## # Sequence_Source <chr>, Validation_Method <chr>, Score <lgl>,
## # BAM_File <lgl>, Sequencer <chr>, Tumor_Sample_UUID <chr>,
## # Matched_Norm_Sample_UUID <chr>, chromosome_name <chr>, start <dbl>,
## # stop <dbl>, reference <chr>, variant <chr>, type <chr>, gene_name <chr>,
## # transcript_name <chr>, transcript_species <chr>, transcript_source <chr>,
## # transcript_version <chr>, strand <dbl>, transcript_status <chr>,
## # trv_type <chr>, c_position <chr>, amino_acid_change <chr>, ucsc_cons <chr>,
## # domain <chr>, all_domains <chr>, deletion_substructures <chr>,
## # transcript_error <chr>, default_gene_name <chr>, gene_name_source <chr>,
## # gene_name_ensembl <chr>, tumor_ref_reads <dbl>, tumor_var_reads <dbl>,
## # tumor_vaf <dbl>, normal_ref_reads <dbl>, normal_var_reads <dbl>,
## # normal_vaf <dbl>, tumor_ref_reads_val <dbl>, tumor_var_reads_val <dbl>,
## # tumor_vaf_val <dbl>, normal_ref_reads_val <dbl>,
## # normal_var_reads_val <dbl>, normal_vaf_val <dbl>, misc_ref_reads_val <dbl>,
## # misc_var_reads_val <dbl>, misc_vaf_val <dbl>
##
## $ucsc.edu_CESC.IlluminaGA_DNASeq_automated.Level_2.1.1.0.somatic.maf
## # A tibble: 39,864 x 50
## Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position
## <chr> <int> <chr> <chr> <chr> <int>
## 1 AHDC1 27245 ucsc.… GRCh37 1 27875174
## 2 IPO13 9670 ucsc.… GRCh37 1 44433064
## 3 ATP5F1 515 ucsc.… GRCh37 1 112002183
## 4 DENND2C 163259 ucsc.… GRCh37 1 115142027
## 5 S100A1 6271 ucsc.… GRCh37 1 153604234
## 6 ARHGEF11 9826 ucsc.… GRCh37 1 156907208
## 7 ADCY10 55811 ucsc.… GRCh37 1 167791359
## 8 ATP2B4 493 ucsc.… GRCh37 1 203693066
## 9 USH2A 7399 ucsc.… GRCh37 1 215848679
## 10 DQX1 165545 ucsc.… GRCh37 2 74751187
## # … with 39,854 more rows, and 44 more variables: End_Position <int>,
## # Strand <chr>, Variant_Classification <chr>, Variant_Type <chr>,
## # Reference_Allele <chr>, Tumor_Seq_Allele1 <chr>, Tumor_Seq_Allele2 <chr>,
## # dbSNP_RS <chr>, dbSNP_Val_Status <lgl>, Tumor_Sample_Barcode <chr>,
## # Matched_Norm_Sample_Barcode <chr>, Match_Norm_Seq_Allele1 <chr>,
## # Match_Norm_Seq_Allele2 <chr>, Tumor_Validation_Allele1 <lgl>,
## # Tumor_Validation_Allele2 <lgl>, Match_Norm_Validation_Allele1 <lgl>,
## # Match_Norm_Validation_Allele2 <lgl>, Verification_Status <chr>,
## # Validation_Status <chr>, Mutation_Status <chr>, Sequencing_Phase <lgl>,
## # Sequence_Source <chr>, Validation_Method <chr>, Score <lgl>,
## # BAM_File <lgl>, Sequencer <chr>, Tumor_Sample_UUID <chr>,
## # Matched_Norm_Sample_UUID <chr>, RNA_Tumor_Sample_Barcode <chr>,
## # RNA_Tumor_Sample_UUID <chr>, RNA_Tumor_Seq_Allele1 <chr>,
## # RNA_Tumor_Seq_Allele2 <chr>, RNA_Normal_Sample_Barcode <lgl>,
## # RNA_Normal_Sample_UUID <lgl>, RNA_Normal_Seq_Allele1 <lgl>,
## # RNA_Normal_Seq_Allele2 <lgl>, Match_Norm_Ref_Count <dbl>,
## # Match_Norm_Alt_Count <dbl>, Tumor_Ref_Count <dbl>, Tumor_Alt_Count <dbl>,
## # RNA_Norm_Ref_Count <lgl>, RNA_Norm_Alt_Count <lgl>,
## # RNA_Tumor_Ref_Count <dbl>, RNA_Tumor_Alt_Count <dbl>
##
## $bcgsc.ca_CESC.IlluminaHiSeq_DNASeq.1.somatic.maf
## # A tibble: 68,621 x 34
## Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position
## <chr> <int> <chr> <chr> <chr> <int>
## 1 COL3A1 1281 bcgsc… GRCh37-li… 2 189873889
## 2 RAB35 11021 bcgsc… GRCh37-li… 12 120534993
## 3 SMC1A 8243 bcgsc… GRCh37-li… X 53439197
## 4 CDK11B 984 bcgsc… GRCh37-li… 1 1572104
## 5 CAMTA1 23261 bcgsc… GRCh37-li… 1 7724942
## 6 PER3 8863 bcgsc… GRCh37-li… 1 7863155
## 7 CSMD2 114784 bcgsc… GRCh37-li… 1 34180259
## 8 BSND 7809 bcgsc… GRCh37-li… 1 55464880
## 9 TUFT1 7286 bcgsc… GRCh37-li… 1 151534633
## 10 IFI16 3428 bcgsc… GRCh37-li… 1 159023487
## # … with 68,611 more rows, and 28 more variables: End_Position <int>,
## # Strand <chr>, Variant_Classification <chr>, Variant_Type <chr>,
## # Reference_Allele <chr>, Tumor_Seq_Allele1 <chr>, Tumor_Seq_Allele2 <chr>,
## # dbSNP_RS <chr>, dbSNP_Val_Status <chr>, Tumor_Sample_Barcode <chr>,
## # Matched_Norm_Sample_Barcode <chr>, Match_Norm_Seq_Allele1 <chr>,
## # Match_Norm_Seq_Allele2 <chr>, Tumor_Validation_Allele1 <chr>,
## # Tumor_Validation_Allele2 <chr>, Match_Norm_Validation_Allele1 <chr>,
## # Match_Norm_Validation_Allele2 <chr>, Verification_Status <chr>,
## # Validation_Status <chr>, Mutation_Status <chr>, Sequencing_Phase <chr>,
## # Sequence_Source <chr>, Validation_Method <chr>, Score <lgl>,
## # BAM_File <lgl>, Sequencer <chr>, Tumor_Sample_UUID <chr>,
## # Matched_Norm_Sample_UUID <chr>
##
## $PR_TCGA_CESC_PAIR_Capture_All_Pairs.aggregated.capture.tcga.uuid.somatic.maf
## # A tibble: 10,020 x 90
## Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position
## <chr> <int> <chr> <dbl> <chr> <dbl>
## 1 CDK11B 984 broad… 37 1 1572104
## 2 CAMTA1 23261 broad… 37 1 7724942
## 3 PER3 8863 broad… 37 1 7863155
## 4 CSMD2 114784 broad… 37 1 34180259
## 5 BSND 7809 broad… 37 1 55464880
## 6 TUFT1 7286 broad… 37 1 151534633
## 7 IFI16 3428 broad… 37 1 159023487
## 8 ADORA1 134 broad… 37 1 203134455
## 9 OPTC 26254 broad… 37 1 203472794
## 10 FLVCR1 28982 broad… 37 1 213032277
## # … with 10,010 more rows, and 84 more variables: End_position <dbl>,
## # Strand <chr>, Variant_Classification <chr>, Variant_Type <chr>,
## # Reference_Allele <chr>, Tumor_Seq_Allele1 <chr>, Tumor_Seq_Allele2 <chr>,
## # dbSNP_RS <chr>, dbSNP_Val_Status <chr>, Tumor_Sample_Barcode <chr>,
## # Matched_Norm_Sample_Barcode <chr>, Match_Norm_Seq_Allele1 <lgl>,
## # Match_Norm_Seq_Allele2 <lgl>, Tumor_Validation_Allele1 <lgl>,
## # Tumor_Validation_Allele2 <lgl>, Match_Norm_Validation_Allele1 <lgl>,
## # Match_Norm_Validation_Allele2 <lgl>, Verification_Status <lgl>,
## # Validation_Status <lgl>, Mutation_Status <chr>, Sequencing_Phase <chr>,
## # Sequence_Source <chr>, Validation_Method <lgl>, Score <lgl>,
## # BAM_file <lgl>, Sequencer <chr>, Tumor_Sample_UUID <chr>,
## # Matched_Norm_Sample_UUID <chr>, Genome_Change <chr>,
## # Annotation_Transcript <chr>, Transcript_Strand <chr>,
## # Transcript_Exon <dbl>, Transcript_Position <chr>, cDNA_Change <chr>,
## # Codon_Change <chr>, Protein_Change <chr>, Other_Transcripts <chr>,
## # Refseq_mRNA_Id <chr>, Refseq_prot_Id <chr>, SwissProt_acc_Id <chr>,
## # SwissProt_entry_Id <chr>, Description <chr>, UniProt_AApos <chr>,
## # UniProt_Region <chr>, UniProt_Site <chr>, UniProt_Natural_Variations <chr>,
## # UniProt_Experimental_Info <chr>, GO_Biological_Process <chr>,
## # GO_Cellular_Component <chr>, GO_Molecular_Function <chr>,
## # COSMIC_overlapping_mutations <chr>, COSMIC_fusion_genes <chr>,
## # COSMIC_tissue_types_affected <chr>, COSMIC_total_alterations_in_gene <dbl>,
## # Tumorscape_Amplification_Peaks <chr>, Tumorscape_Deletion_Peaks <chr>,
## # TCGAscape_Amplification_Peaks <chr>, TCGAscape_Deletion_Peaks <chr>,
## # DrugBank <chr>, ref_context <chr>, gc_content <dbl>,
## # CCLE_ONCOMAP_overlapping_mutations <chr>,
## # CCLE_ONCOMAP_total_mutations_in_gene <dbl>, CGC_Mutation_Type <chr>,
## # CGC_Translocation_Partner <chr>, CGC_Tumor_Types_Somatic <chr>,
## # CGC_Tumor_Types_Germline <chr>, CGC_Other_Diseases <chr>,
## # DNARepairGenes_Role <chr>, FamilialCancerDatabase_Syndromes <chr>,
## # MUTSIG_Published_Results <chr>, OREGANNO_ID <chr>, OREGANNO_Values <chr>,
## # t_alt_count <int>, t_ref_count <int>, validation_status <lgl>,
## # validation_method <lgl>, validation_tumor_sample <lgl>,
## # validation_alt_allele <lgl>, pox <dbl>, qox <dbl>, pox_cutoff <dbl>,
## # isArtifactMode <dbl>, oxoGCut <dbl>
##
## $gsc_CESC_pairs.aggregated.capture.tcga.uuid.automated.somatic.maf
## # A tibble: 97,933 x 90
## Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position
## <chr> <int> <chr> <dbl> <chr> <dbl>
## 1 SLC8A1 6546 broad… 37 2 40405622
## 2 RP11-156P1… 0 broad… 37 17 45125593
## 3 PDE3A 5139 broad… 37 12 20522788
## 4 HLA-V 0 broad… 37 6 29760111
## 5 HHLA1 10086 broad… 37 8 133089975
## 6 PANX2 56666 broad… 37 22 50615969
## 7 MIR146B 0 broad… 37 10 104196339
## 8 ZNF775 285971 broad… 37 7 150095001
## 9 LCE2C 353140 broad… 37 1 152648817
## 10 RPLP0 6175 broad… 37 12 120635255
## # … with 97,923 more rows, and 84 more variables: End_position <dbl>,
## # Strand <chr>, Variant_Classification <chr>, Variant_Type <chr>,
## # Reference_Allele <chr>, Tumor_Seq_Allele1 <chr>, Tumor_Seq_Allele2 <chr>,
## # dbSNP_RS <chr>, dbSNP_Val_Status <chr>, Tumor_Sample_Barcode <chr>,
## # Matched_Norm_Sample_Barcode <chr>, Match_Norm_Seq_Allele1 <lgl>,
## # Match_Norm_Seq_Allele2 <lgl>, Tumor_Validation_Allele1 <lgl>,
## # Tumor_Validation_Allele2 <lgl>, Match_Norm_Validation_Allele1 <lgl>,
## # Match_Norm_Validation_Allele2 <lgl>, Verification_Status <lgl>,
## # Validation_Status <chr>, Mutation_Status <chr>, Sequencing_Phase <chr>,
## # Sequence_Source <chr>, Validation_Method <chr>, Score <lgl>,
## # BAM_file <lgl>, Sequencer <chr>, Tumor_Sample_UUID <chr>,
## # Matched_Norm_Sample_UUID <chr>, Genome_Change <chr>,
## # Annotation_Transcript <chr>, Transcript_Strand <chr>,
## # Transcript_Exon <dbl>, Transcript_Position <dbl>, cDNA_Change <chr>,
## # Codon_Change <chr>, Protein_Change <chr>, Other_Transcripts <chr>,
## # Refseq_mRNA_Id <chr>, Refseq_prot_Id <chr>, SwissProt_acc_Id <chr>,
## # SwissProt_entry_Id <chr>, Description <chr>, UniProt_AApos <dbl>,
## # UniProt_Region <chr>, UniProt_Site <lgl>, UniProt_Natural_Variations <chr>,
## # UniProt_Experimental_Info <chr>, GO_Biological_Process <chr>,
## # GO_Cellular_Component <chr>, GO_Molecular_Function <chr>,
## # COSMIC_overlapping_mutations <chr>, COSMIC_fusion_genes <chr>,
## # COSMIC_tissue_types_affected <chr>, COSMIC_total_alterations_in_gene <dbl>,
## # Tumorscape_Amplification_Peaks <chr>, Tumorscape_Deletion_Peaks <chr>,
## # TCGAscape_Amplification_Peaks <chr>, TCGAscape_Deletion_Peaks <chr>,
## # DrugBank <chr>, ref_context <chr>, gc_content <dbl>,
## # CCLE_ONCOMAP_overlapping_mutations <chr>,
## # CCLE_ONCOMAP_total_mutations_in_gene <dbl>, CGC_Mutation_Type <chr>,
## # CGC_Translocation_Partner <chr>, CGC_Tumor_Types_Somatic <chr>,
## # CGC_Tumor_Types_Germline <chr>, CGC_Other_Diseases <chr>,
## # DNARepairGenes_Role <chr>, FamilialCancerDatabase_Syndromes <chr>,
## # MUTSIG_Published_Results <chr>, OREGANNO_ID <chr>, OREGANNO_Values <chr>,
## # t_alt_count <int>, t_ref_count <int>, validation_alt_allele <lgl>,
## # validation_method <lgl>, validation_status <lgl>,
## # validation_tumor_sample <lgl>, pox <dbl>, qox <dbl>, pox_cutoff <dbl>,
## # isArtifactMode <dbl>, oxoGCut <dbl>
##
## attr(,"split_type")
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