Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----Load, message=FALSE------------------------------------------------------
library(SigsPack)
## -----------------------------------------------------------------------------
if (require(BSgenome.Hsapiens.UCSC.hg19)) {
sample <- vcf2mut_cat(
system.file("extdata", "example.vcf.gz", package="SigsPack"),
BSgenome.Hsapiens.UCSC.hg19
)
}
## -----------------------------------------------------------------------------
data("cosmicSigs")
cats <- create_mut_catalogues(10, 500, P=cosmicSigs, sig_set = c(2,6,15,27))
knitr::kable(head(cats[['catalogues']]))
## -----------------------------------------------------------------------------
reps <- bootstrap_mut_catalogues(n = 1000, original = cats[["catalogues"]][,1])
# using only signatures 4, 17, 23 and 30 for signature estimation
sigs <- signature_exposure(reps, sig_set = c(4,17,23,30))
print(sigs$exposures[,1])
## ---- fig.show='hold', fig.height=7, fig.width=7------------------------------
report <- summarize_exposures(reps[,1])
knitr::kable(
head(report)
)
## -----------------------------------------------------------------------------
if (require(BSgenome.Hsapiens.UCSC.hg19)){
genome_contexts <- get_context_freq(BSgenome.Hsapiens.UCSC.hg19)
exome_contexts <- get_context_freq(
BSgenome.Hsapiens.UCSC.hg19,
system.file("extdata", "example.bed.gz", package="SigsPack")
)
normalized_mut_cat <- SigsPack::normalize(sample, exome_contexts, hg19context_freq)
}
## ---- fig.show='hold', fig.height=7, fig.width=7------------------------------
if (require(BSgenome.Hsapiens.UCSC.hg19)) {
sigs_norm <- signature_exposure(sum(sample) * normalized_mut_cat)
report_norm <- summarize_exposures(normalized_mut_cat, m=sum(sample))
reps_norm <- bootstrap_mut_catalogues(
n=1000,
original=normalized_mut_cat,
m=sum(sample)
)
}
## -----------------------------------------------------------------------------
sessionInfo()
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