9 Datasets
9.1 Reference annotation
sigminer stores many reference annotation datasets for internal calculation. It can be exported for other usage either bydata() orget_genome_annotation().
Currently, there are the following datasets:
centromeres.hg19centromeres.hg38chromsize.hg19chromsize.hg38cytobands.hg19cytobands.hg38
An example is given as below:
data("centromeres.hg19")head(centromeres.hg19)## chrom left.base right.base## 1 chr1 121535434 124535434## 2 chr2 92326171 95326171## 3 chr3 90504854 93504854## 4 chr4 49660117 52660117## 5 chr5 46405641 49405641## 6 chr6 58830166 61830166get_genome_annotation() can better control the returneddata.frame.
get_genome_annotation( data_type="chr_size", chrs=c("chr1","chr10","chr20"), genome_build="hg19")## chrom size## 1 chr1 249250621## 2 chr10 135534747## 3 chr20 63025520More see?get_genome_annotation.
9.2 Copy number components setting
DatasetCN.features is a predefined component data table for identifying copy number signatures by method “Wang”.Users can define a custom table with similar structure and pass it to function likesig_tally().
Detail about how to generate this dataset can be viewed athttps://github.com/ShixiangWang/sigminer/blob/master/data-raw/CN-features.R.
CN.features## feature component label min max## 1: BP10MB BP10MB[0] point 0 0## 2: BP10MB BP10MB[1] point 1 1## 3: BP10MB BP10MB[2] point 2 2## 4: BP10MB BP10MB[3] point 3 3## 5: BP10MB BP10MB[4] point 4 4## 6: BP10MB BP10MB[5] point 5 5## 7: BP10MB BP10MB[>5] range 5 Inf## 8: BPArm BPArm[0] point 0 0## 9: BPArm BPArm[1] point 1 1## 10: BPArm BPArm[2] point 2 2## 11: BPArm BPArm[3] point 3 3## 12: BPArm BPArm[4] point 4 4## 13: BPArm BPArm[5] point 5 5## 14: BPArm BPArm[6] point 6 6## 15: BPArm BPArm[7] point 7 7## 16: BPArm BPArm[8] point 8 8## 17: BPArm BPArm[9] point 9 9## 18: BPArm BPArm[10] point 10 10## 19: BPArm BPArm[>10 & <=20] range 10 20## 20: BPArm BPArm[>20 & <=30] range 20 30## 21: BPArm BPArm[>30] range 30 Inf## 22: CN CN[0] point 0 0## 23: CN CN[1] point 1 1## 24: CN CN[2] point 2 2## 25: CN CN[3] point 3 3## 26: CN CN[4] point 4 4## 27: CN CN[>4 & <=8] range 4 8## 28: CN CN[>8] range 8 Inf## 29: CNCP CNCP[0] point 0 0## 30: CNCP CNCP[1] point 1 1## 31: CNCP CNCP[2] point 2 2## 32: CNCP CNCP[3] point 3 3## 33: CNCP CNCP[4] point 4 4## 34: CNCP CNCP[>4 & <=8] range 4 8## 35: CNCP CNCP[>8] range 8 Inf## 36: OsCN OsCN[0] point 0 0## 37: OsCN OsCN[1] point 1 1## 38: OsCN OsCN[2] point 2 2## 39: OsCN OsCN[3] point 3 3## 40: OsCN OsCN[4] point 4 4## 41: OsCN OsCN[>4 & <=10] range 4 10## 42: OsCN OsCN[>10] range 10 Inf## 43: SS SS[<=2] range -Inf 2## 44: SS SS[>2 & <=3] range 2 3## 45: SS SS[>3 & <=4] range 3 4## 46: SS SS[>4 & <=5] range 4 5## 47: SS SS[>5 & <=6] range 5 6## 48: SS SS[>6 & <=7] range 6 7## 49: SS SS[>7 & <=8] range 7 8## 50: SS SS[>8] range 8 Inf## 51: NC50 NC50[<=2] range -Inf 2## 52: NC50 NC50[3] point 3 3## 53: NC50 NC50[4] point 4 4## 54: NC50 NC50[5] point 5 5## 55: NC50 NC50[6] point 6 6## 56: NC50 NC50[7] point 7 7## 57: NC50 NC50[>7] range 7 Inf## 58: BoChr BoChr[1] point 1 1## 59: BoChr BoChr[2] point 2 2## 60: BoChr BoChr[3] point 3 3## 61: BoChr BoChr[4] point 4 4## 62: BoChr BoChr[5] point 5 5## 63: BoChr BoChr[6] point 6 6## 64: BoChr BoChr[7] point 7 7## 65: BoChr BoChr[8] point 8 8## 66: BoChr BoChr[9] point 9 9## 67: BoChr BoChr[10] point 10 10## 68: BoChr BoChr[11] point 11 11## 69: BoChr BoChr[12] point 12 12## 70: BoChr BoChr[13] point 13 13## 71: BoChr BoChr[14] point 14 14## 72: BoChr BoChr[15] point 15 15## 73: BoChr BoChr[16] point 16 16## 74: BoChr BoChr[17] point 17 17## 75: BoChr BoChr[18] point 18 18## 76: BoChr BoChr[19] point 19 19## 77: BoChr BoChr[20] point 20 20## 78: BoChr BoChr[21] point 21 21## 79: BoChr BoChr[22] point 22 22## 80: BoChr BoChr[23] point 23 23## feature component label min max