somaticsignature (mutation signature)

mutation.signature_tutorial20190418.r

https://bioconductor.org/packages/release/bioc/html/SomaticSignatures.html

SomaticSignatures

The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure...

bioconductor.org

http://www.bioconductor.org/packages/devel/bioc/vignettes/SomaticSignatures/inst/doc/SomaticSignatures-vignette.html

Inferring Somatic Signatures from Single Nucleotide Variant Calls

www.bioconductor.org

 

hg19 reference genome

source("https://bioconductor.org/biocLite.R")
biocLite("BSgenome.Hsapiens.UCSC.hg19")

library(VariantAnnotation)
library(SomaticSignatures)
install.packages("data.table")
library(data.table)

#Load the SNV-VCF file into R
#Combine the matrix you should one column for sample name
vcf <- VRanges(
  seqnames = g458$CHROM, # chromosome
  ranges = IRanges(start = g458$POS,end = g458$POS), # Position
  ref = g458$REF, # Reference
  alt=g458$ALT, # Alteration
  sampleNames =sample(rep(paste0('g',1:10),nrow(g458)),nrow(g458)), # Sample name
  study=sample(rep(paste0('a',1:3),nrow(g458)),nrow(g458)) # put them same name unless you want to analyze different tissues
    study는 넣지말것!
 )
library(BSgenome.Hsapiens.UCSC.hg19) #hg19 reference genome
sca_motifs = mutationContext(vcf, BSgenome.Hsapiens.UCSC.hg19)
sca_mm2 = motifMatrix(sca_motifs, normalize = TRUE)
plotMutationSpectrum(sca_motifs,'study') # You will see overall mutation spectrum histogram
n_sigs = 2:10 # define number of signatures to check
gof_nmf = assessNumberSignatures(sca_mm2, n_sigs, nReplicates = 3) # get stability of signature
plotNumberSignatures(gof_nmf) 

n_sigs = 6 # decide optimal number of signature
sigs_nmf2 = identifySignatures(sca_mm2, n_sigs, nmfDecomposition)
plotSignatures(sigs_nmf2)
plotSamples(sigs_nmf2)