genpb (version 0.0.14)

hbvsnp: comparison of heterozygous binding locations for CTCF with known SNP locations

Description

comparison of heterozygous binding locations for CTCF with known SNP locations

Usage

data(hbvsnp)

format

The format is: List of 22 $ chr22:List of 22 ..$ :List of 2 .. ..$ onsnp :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. ..@ seqnames :Formal class 'Rle' [package "IRanges"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 22 levels "chr10","chr11",..: 14 .. .. .. .. .. ..@ lengths : int 116 .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. ..@ start : int [1:116] 17264904 17392539 17392558 18225318 18268130 18884091 18896087 18942199 19768045 19949952 ... .. .. .. .. .. ..@ width : int [1:116] 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. .. ..@ NAMES : chr [1:116] "NA06990_2.bam" "NA06990_2.bam" "NA06990_2.bam" "NA06990_2.bam" ... .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ strand :Formal class 'Rle' [package "IRanges"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 3 .. .. .. .. .. ..@ lengths : int 116 .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "IRanges"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 116 .. .. .. .. .. ..@ listData :List of 6 .. .. .. .. .. .. ..$ A : int [1:116] 5 0 14 0 0 10 0 0 0 8 ... .. .. .. .. .. .. ..$ C : int [1:116] 0 10 0 24 15 5 8 11 6 0 ... .. .. .. .. .. .. ..$ G : int [1:116] 6 21 0 0 0 0 0 0 0 21 ... .. .. .. .. .. .. ..$ T : int [1:116] 0 0 16 11 9 0 18 5 5 0 ... .. .. .. .. .. .. ..$ medQ: num [1:116] 64 62 64 62 63 64 62 51 62 63 ... .. .. .. .. .. .. ..$ madQ: num [1:116] 0 2.97 1.48 2.97 1.48 ... .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomicRanges"] with 4 slots .. .. .. .. .. ..@ seqnames : chr [1:22] "chr10" "chr11" "chr12" "chr13" ... .. .. .. .. .. ..@ seqlengths : int [1:22] 135534747 135006516 133851895 115169878 107349540 102531392 90354753 81195210 78077248 59128983 ... .. .. .. .. .. ..@ is_circular: logi [1:22] NA NA NA NA NA NA ... .. .. .. .. .. ..@ genome : chr [1:22] "GRCh37.p5" "GRCh37.p5" "GRCh37.p5" "GRCh37.p5" ... .. .. .. ..@ metadata :List of 3 .. .. .. .. ..$ protocolDoc : chr "http://genome.ucsc.edu/ENCODE/protocols/cell/human/Stam_15_protocols.pdf" .. .. .. .. ..$ relevantPMIDs: chr "22307276" .. .. .. .. ..$ relevantMIAME:List of 1 .. .. .. .. .. ..$ 22307276:Formal class 'MIAME' [package "Biobase"] with 13 slots .. .. .. .. .. .. .. ..@ name : chr "Degner JF" .. .. .. .. .. .. .. ..@ lab : chr "Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA." .. .. .. .. .. .. .. ..@ contact : chr "" .. .. .. .. .. .. .. ..@ title : chr "DNaseI sensitivity QTLs are a major determinant of human expression variation." .. .. .. .. .. .. .. ..@ abstract : chr "The mapping of expression quantitative trait loci (eQTLs) has emerged as an important tool for linking genetic variation to cha"| __truncated__ .. .. .. .. .. .. .. ..@ url : chr "" .. .. .. .. .. .. .. ..@ pubMedIds : chr "22307276" .. .. .. .. .. .. .. ..@ samples : list() .. .. .. .. .. .. .. ..@ hybridizations : list() .. .. .. .. .. .. .. ..@ normControls : list() .. .. .. .. .. .. .. ..@ preprocessing : list() .. .. .. .. .. .. .. ..@ other : list() .. .. .. .. .. .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. .. .. .. .. .. ..@ .Data:List of 2 .. .. .. .. .. .. .. .. .. .. ..$ : int [1:3] 1 0 0 .. .. .. .. .. .. .. .. .. .. ..$ : int [1:3] 1 1 0 .. ..$ offsnp:Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. ..@ seqnames :Formal class 'Rle' [package "IRanges"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 22 levels "chr10","chr11",..: 14 .. .. .. .. .. ..@ lengths : int 160 .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots

Details

22 BAM files were analyzed for heterozygous binding of CTCF to DNA on 15 different cell lines. Locations of heterozygous binding at call counts for distinct nucleotides of 4 or greater were compared with 2012.06.08 dbSNP locations. This structure has chromosome-specific, individual-specific ranges for on-SNP and off-SNP heterozygous binding events.

Examples

data(hbvsnp)
length(hbvsnp)
length(hbvsnp[[1]])