signature_commands.txt

cd ~/somatic/somatic_signatures


pwd

ls

R

library(SomaticSignatures)

library(BSgenome.Hsapiens.UCSC.hg19)

library(ggplot2)

library(Cairo)

setwd(”~/somatic/somatic_signatures”)

files <- list.files("~/somatic/somatic_signatures", pattern="vcf$", full.names=TRUE)

files

vranges <- lapply(files, function(v) readVcfAsVRanges(v,"hg19"))


vranges.cat <- do.call(c,vranges)


vranges.cat



vranges.cat <- ucsc(vranges.cat)

print(table(sampleNames(vranges.cat)))

mc <- mutationContext(vranges.cat, BSgenome.Hsapiens.UCSC.hg19)

mm <- motifMatrix(mc, group = "sampleNames", normalize=TRUE)

dim(mm)

gof_nmf <- assessNumberSignatures(mm, 2:10, nReplicates = 5)


Cairo(file="plotNumberOfSignatures.pdf", type="pdf", units="in", width=9, height=8, dpi=72)


plotNumberSignatures(gof_nmf)


dev.off()

sigs_nmf = identifySignatures(mm, 3, nmfDecomposition)

Cairo(file="plot3Signatures.pdf", type="pdf", units="in", width=10, height=8, dpi=72)


plotSignatures(sigs_nmf,normalize=TRUE, percent=FALSE) + ggtitle("Somatic Signatures: NMF - Barchart") + scale_fill_brewer(palette = "Set2")


dev.off()

Cairo(file="PlotSampleContribution3Signatures.pdf", type="pdf", units="in", width=9, height=6, dpi=72)


plotSamples(sigs_nmf, normalize=TRUE) + scale_y_continuous(breaks=seq(0, 1, 0.2), expand = c(0,0))+ theme(axis.text.x = element_text(size=6))


dev.off()

#advanced
sigs_nmf = identifySignatures(mm, 4, nmfDecomposition)

Cairo(file="plot4Signatures.pdf", type="pdf", units="in", width=10, height=8, dpi=72)


plotSignatures(sigs_nmf,normalize=TRUE, percent=FALSE) + ggtitle("Somatic Signatures: NMF - Barchart") + scale_fill_brewer(palette = "Set2")


dev.off()

Cairo(file="PlotSampleContribution4Signatures.pdf", type="pdf", units="in", width=9, height=6, dpi=72)


plotSamples(sigs_nmf, normalize=TRUE) + scale_y_continuous(breaks=seq(0, 1, 0.2), expand = c(0,0))+ theme(axis.text.x = element_text(size=6))


dev.off()


quit()

n