Nothing
## ----results='hide', echo=FALSE, message=FALSE, warning=FALSE-----------------
set.seed(42)
library(knitr)
opts_knit$set(
self.contained = TRUE,
upload.fun = image_uri
)
opts_chunk$set(
dev = 'png',
dpi = 300,
out.width = "700px",
out.height = "700px"
)
## ----eval=FALSE---------------------------------------------------------------
# install.packages("BiocManager")
# BiocManager::install("signeR")
## ----results='hide', message=FALSE--------------------------------------------
library(signeR)
## ----eval=FALSE---------------------------------------------------------------
# library(VariantAnnotation)
#
# # BSgenome, equivalent to the one used on the variant call
# library(BSgenome.Hsapiens.UCSC.hg19)
#
# vcfobj <- readVcf("/path/to/a/file.vcf", "hg19")
# mut <- genCountMatrixFromVcf(BSgenome.Hsapiens.UCSC.hg19, vcfobj)
## ----eval=FALSE---------------------------------------------------------------
# mut = matrix(ncol=96,nrow=0)
# for(i in vcf_files) {
# vo = readVcf(i, "hg19")
# # sample name (should pick up from the vcf automatically if available)
# # colnames(vo) = i
# m0 = genCountMatrixFromVcf(mygenome, vo)
# mut = rbind(mut, m0)
# }
# dim(mut) # matrix with all samples
## ----eval=FALSE---------------------------------------------------------------
# library(rtracklayer)
#
# target_regions <- import(con="/path/to/a/target.bed", format="bed")
# opp <- genOpportunityFromGenome(BSgenome.Hsapiens.UCSC.hg19,
# target_regions, nsamples=nrow(mut))
## ----eval=FALSE---------------------------------------------------------------
# library(Rsamtools)
#
# # make sure /path/to/genome.fasta.fai exists !
# # you can use "samtools faidx" command to create it
# mygenome <- FaFile("/path/to/genome.fasta")
#
# mut <- genCountMatrixFromVcf(mygenome, vcfobj)
# opp <- genOpportunityFromGenome(mygenome, target_regions)
#
## -----------------------------------------------------------------------------
mut <- read.table(system.file("extdata","21_breast_cancers.mutations.txt",
package="signeR"), header=TRUE, check.names=FALSE)
opp <- read.table(system.file("extdata","21_breast_cancers.opportunity.txt",
package="signeR"))
## ----eval=FALSE---------------------------------------------------------------
# signatures <- signeR(M=mut, Opport=opp)
## ----eval=FALSE---------------------------------------------------------------
# signatures <- signeR(M=mut, Opport=opp, nlim=c(2,11))
## ----results='hide', message=FALSE--------------------------------------------
signatures <- signeR(M=mut, Opport=opp, nsig=5, main_eval=100, EM_eval=50, EMit_lim=20)
## ----eval=FALSE---------------------------------------------------------------
# BICboxplot(signatures)
## ----echo=FALSE, results='asis'-----------------------------------------------
cat(sprintf("<img src=\"%s\" />\n",image_uri("Model_selection_BICs.png")))
## -----------------------------------------------------------------------------
Paths(signatures$SignExposures)
## -----------------------------------------------------------------------------
SignPlot(signatures$SignExposures)
## -----------------------------------------------------------------------------
SignHeat(signatures$SignExposures)
## -----------------------------------------------------------------------------
ExposureBoxplot(signatures$SignExposures)
## -----------------------------------------------------------------------------
ExposureBarplot(signatures$SignExposures)
## -----------------------------------------------------------------------------
ExposureHeat(signatures$SignExposures)
## -----------------------------------------------------------------------------
# group labels, respective to each row of the mutation count matrix
BRCA_labels <- c("wt","BRCA1+","BRCA2+","BRCA1+","BRCA2+","BRCA1+","BRCA1+",
"wt","wt","wt","wt","BRCA1+","wt","BRCA2+","BRCA2+","wt","wt","wt",
"wt","wt","wt")
diff_exposure <- DiffExp(signatures$SignExposures, labels=BRCA_labels)
## -----------------------------------------------------------------------------
# pvalues
diff_exposure$Pvquant
## -----------------------------------------------------------------------------
# most exposed group
diff_exposure$MostExposed
## -----------------------------------------------------------------------------
# note that BRCA_labels [15],[20] and [21] are set to NA
BRCA_labels <- c("wt","BRCA+","BRCA+","BRCA+","BRCA+","BRCA+","BRCA+","wt","wt",
"wt","wt","BRCA+","wt","BRCA+",NA,"wt","wt","wt","wt",NA,NA)
Class <- Classify(signatures$SignExposures, labels=BRCA_labels)
## -----------------------------------------------------------------------------
# Final assignments
Class$class
# Relative frequencies of assignment to selected groups
Class$freq
# All assigment frequencies
Class$allfreqs
## -----------------------------------------------------------------------------
citation("signeR")
## -----------------------------------------------------------------------------
sessionInfo()
## -----------------------------------------------------------------------------
print(names(dev.cur()))
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