cosmicNCBI36: COSMIC data mapped to NCBI36 (hg18)

In seandavi/COSMIC.build57: Data package containing COSMIC Build 37 data

Description

COSMIC data mapped to NCBI36 (hg18)

Usage

data(cosmicNCBI36)

Format

The format is: Formal class 'GRanges' [package "GenomicRanges"] with 6 slots ..@ seqnames :Formal class 'Rle' [package "IRanges"] with 4 slots .. .. ..@ values : Factor w/ 24 levels "chr1","chr10",..: 2 4 15 18 4 12 21 19 22 9 ... .. .. ..@ lengths : int [1:8393] 1 6 1 1 3 1 1 4 1 5 ... .. .. ..@ elementMetadata: NULL .. .. ..@ metadata : list() ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. ..@ start : int [1:34281] 52245937 9150431 9150104 9116623 9121242 8912192 8882264 41418956 139332477 51987696 ... .. .. ..@ width : int [1:34281] 1 1 1 1 1 1 1 1 1 1 ... .. .. ..@ NAMES : NULL .. .. ..@ elementType : chr "integer" .. .. ..@ elementMetadata: NULL .. .. ..@ metadata : list() ..@ strand :Formal class 'Rle' [package "IRanges"] with 4 slots .. .. ..@ values : Factor w/ 3 levels "+","-","*": 3 .. .. ..@ lengths : int 34281 .. .. ..@ elementMetadata: NULL .. .. ..@ metadata : list() ..@ elementMetadata:Formal class 'DataFrame' [package "IRanges"] with 6 slots .. .. ..@ rownames : NULL .. .. ..@ nrows : int 34281 .. .. ..@ listData :List of 24 .. .. .. ..$ Gene.name : Factor w/ 15198 levels "A1CF","A2M","A2ML1",..: 1 2 2 2 2 3 3 4 5 6 ... .. .. .. ..$ Accession.Number : Factor w/ 15158 levels "AB023190","AB051467.1",..: 9114 10964 10964 10964 10964 4598 4598 1096 801 261 ... .. .. .. ..$ HGNC.ID : int [1:34281] 24086 7 7 7 7 23336 23336 18149 17968 13666 ... .. .. .. ..$ Sample.name : Factor w/ 153739 levels " HOG06-122"," HOG06-1221",..: 118608 118525 148952 148957 148996 149344 149368 118524 118566 149234 ... .. .. .. ..$ ID_sample : int [1:34281] 1312984 1312971 1287214 1287216 1287244 1475013 1474986 1312970 1312975 1474963 ... .. .. .. ..$ ID_tumour : int [1:34281] 1223893 1223880 1198492 1198494 1198522 1398712 1398685 1223879 1223884 1398662 ... .. .. .. ..$ Primary.site : Factor w/ 43 levels "Fallopian tube",..: 8 8 8 8 8 21 21 8 8 21 ... .. .. .. ..$ Site.subtype : Factor w/ 172 levels "NS","abdomen",..: 16 16 16 16 16 1 1 16 16 1 ... .. .. .. ..$ Primary.histology : Factor w/ 84 levels "Ewings_sarcoma-peripheral_primitive_neuroectodermal_tumour",..: 40 40 40 40 40 23 23 40 40 23 ... .. .. .. ..$ Histology.subtype : Factor w/ 399 levels "ACTH","ACTH-FSH",..: 82 82 82 82 82 351 351 33 82 351 ... .. .. .. ..$ Genome.wide.screen : Factor w/ 3 levels "","n","y": 1 1 1 1 1 3 3 1 1 3 ... .. .. .. ..$ Mutation.ID : int [1:34281] 40879 39653 35965 35963 35964 78858 79446 39410 41045 79447 ... .. .. .. ..$ Mutation.CDS : Factor w/ 38881 levels "","Intronic",..: 38446 37309 1522 22775 20223 23591 37411 37952 19219 6125 ... .. .. .. ..$ Mutation.AA : Factor w/ 54163 levels "","p.","p.(1409)ins6",..: 9502 47270 15450 11774 46083 36292 1714 50231 215 44522 ... .. .. .. ..$ Mutation.Description : Factor w/ 15 levels "Complex - compound substitution",..: 11 11 11 11 13 12 13 11 13 13 ... .. .. .. ..$ Mutation.zygosity : Factor w/ 3 levels "het","hom","unk": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. ..$ Mutation.NCBI36.genome.position: Factor w/ 34282 levels "","10:100001319-100001319",..: 668 5102 5101 5098 5099 5086 5085 18559 23172 4666 ... .. .. .. ..$ Mutation.NCBI36.strand : Factor w/ 3 levels "","+","-": 3 3 3 3 3 2 2 3 3 3 ... .. .. .. ..$ Mutation.GRCh37.strand : Factor w/ 3 levels "","+","-": 3 3 3 3 3 2 2 3 3 3 ... .. .. .. ..$ Mutation.somatic.status : Factor w/ 6 levels "Confirmed germline variant",..: 2 2 2 2 2 2 2 2 2 2 ... .. .. .. ..$ Pubmed_PMID : int [1:34281] 18772396 18772396 18772890 18772890 18772890 21720365 21720365 18772396 18772396 21720365 ... .. .. .. ..$ Sample.source : Factor w/ 27 levels "NS","autopsy - NOS",..: 23 23 24 24 24 1 1 27 27 1 ... .. .. .. ..$ Tumour.origin : Factor w/ 8 levels "NS","adenoma adjacent to primary tumour",..: 7 5 6 7 7 5 5 5 5 5 ... .. .. .. ..$ Comments : Factor w/ 2723 levels "","Age at tumour recurrence:1 year after diagnosis of TMD",..: 1002 1002 1 1 1 1 1 1002 1002 1 ... .. .. ..@ elementType : chr "ANY" .. .. ..@ elementMetadata: NULL .. .. ..@ metadata : list() ..@ seqinfo :Formal class 'Seqinfo' [package "GenomicRanges"] with 4 slots .. .. ..@ seqnames : chr [1:24] "chr1" "chr10" "chr11" "chr12" ... .. .. ..@ seqlengths : int [1:24] NA NA NA NA NA NA NA NA NA NA ... .. .. ..@ is_circular: logi [1:24] NA NA NA NA NA NA ... .. .. ..@ genome : chr [1:24] NA NA NA NA ... ..@ metadata : list()

Details

The data are in a GRanges object with elementMetadata from the original download. Note that some of the ranges are large, so one may need to filter when looking for overlapping variants.

Source

ftp://ftp.sanger.ac.uk/pub/CGP/cosmic/data_export/CosmicMutantExport_v57_180112.tsv

References

http://www.sanger.ac.uk/genetics/CGP/cosmic/

Examples

data(cosmicGRCh37)

seandavi/COSMIC.build57 documentation built on May 29, 2019, 4:28 p.m.