Nothing
## ----style, eval=TRUE, echo=FALSE, results="asis"--------------------------
BiocStyle::latex()
## ----include=FALSE---------------------------------------------------------
knitr::opts_chunk$set(concordance=TRUE,
resize.width="0.45\\textwidth",
fig.align='center',
tidy = FALSE,
message=FALSE)
## ----echo=FALSE, results='asis'--------------------------------------------
primerFile = system.file("extdata/primer.fa",
package="FourCSeq")
writeLines(readLines(primerFile))
## ----eval=FALSE------------------------------------------------------------
# system.file("extdata/python/demultiplex.py", package="FourCSeq")
## ----LoadLibraries, eval=TRUE----------------------------------------------
library(FourCSeq)
## ----filePaths, cache=TRUE-------------------------------------------------
referenceGenomeFile = system.file("extdata/dm3_chr2L_1-6900.fa",
package="FourCSeq")
referenceGenomeFile
bamFilePath = system.file("extdata/bam",
package="FourCSeq")
bamFilePath
primerFile = system.file("extdata/primer.fa",
package="FourCSeq")
primerFile
## ----results='hide'--------------------------------------------------------
writeLines(readLines(primerFile))
## ----echo=FALSE,results='asis'---------------------------------------------
writeLines(readLines(primerFile))
## ----metadata, cache=TRUE--------------------------------------------------
metadata <- list(projectPath = "exampleData",
fragmentDir = "re_fragments",
referenceGenomeFile = referenceGenomeFile,
reSequence1 = "GATC",
reSequence2 = "CATG",
primerFile = primerFile,
bamFilePath = bamFilePath)
metadata
## ----colData, eval=TRUE, cache=TRUE----------------------------------------
colData <- DataFrame(viewpoint = "testdata",
condition = factor(rep(c("WE_68h", "MESO_68h", "WE_34h"),
each=2),
levels = c("WE_68h", "MESO_68h", "WE_34h")),
replicate = rep(c(1, 2),
3),
bamFile = c("CRM_ap_ApME680_WE_6-8h_1_testdata.bam",
"CRM_ap_ApME680_WE_6-8h_2_testdata.bam",
"CRM_ap_ApME680_MESO_6-8h_1_testdata.bam",
"CRM_ap_ApME680_MESO_6-8h_2_testdata.bam",
"CRM_ap_ApME680_WE_3-4h_1_testdata.bam",
"CRM_ap_ApME680_WE_3-4h_2_testdata.bam"),
sequencingPrimer="first")
colData
## ----ObjectInitialization, eval=TRUE, cache=TRUE, dependson=c("filePaths", "metadata", "colData")----
fc <- FourC(colData, metadata)
fc
## ----AddingFragmentReference, eval=TRUE, cache=TRUE, dependson=c("ObjectInitialization")----
fc <- addFragments(fc)
fc
rowRanges(fc)
## ----AddingViewpointFragmentInformation, eval=TRUE, cache=TRUE, dependson=c("ObjectInitialization")----
findViewpointFragments(fc)
fc <- addViewpointFrags(fc)
## ----AddingViewpointFragmentInformationManually, eval=FALSE----------------
# colData(fc)$chr = "chr2L"
# colData(fc)$start = 6027
# colData(fc)$end = 6878
## ----CountingReadOverlapsWithFragments, eval=TRUE, cache=TRUE, dependson=c("ObjectInitialization")----
fc <- countFragmentOverlaps(fc, trim=4, minMapq=30)
## ----combineFragEnds, eval=TRUE, cache=TRUE, dependson=c("CountingReadOverlapsWithFragments")----
fc <- combineFragEnds(fc)
## --------------------------------------------------------------------------
library(SummarizedExperiment)
fc
assays(fc)
head(assay(fc, "counts"))
## --------------------------------------------------------------------------
data(fc)
metadata(fc)$projectPath
metadata(fc)$projectPath <- "exampleData"
fc
assays(fc)
head(assay(fc, "counts"))
## ----WriteTrackFiles, eval=TRUE, cache=TRUE, dependson=c("CountingReadOverlapsWithFragments")----
writeTrackFiles(fc)
writeTrackFiles(fc, format='bedGraph')
## ----SmoothOverFragments, eval=TRUE, cache=TRUE, dependson=c("CountingReadOverlapsWithFragments")----
fc <- smoothCounts(fc)
fc
## ----correlation, dev.args=list(pointsize=16), dependson=c("CountingReadOverlapsWithFragments")----
plotScatter(fc[,c("ap_WE_68h_1", "ap_WE_68h_2")],
xlab="Replicate1", ylab="Replicate2", asp=1)
## ----CalculateZScores, eval=TRUE, cache=TRUE, dependson=c("CountingReadOverlapsWithFragments"), results='hide'----
fcf <- getZScores(fc)
fcf
## ----zScoreDistribution, eval=TRUE, cache=TRUE, fig.show='hold', dependson=c("CalculateZScores")----
zScore <- SummarizedExperiment::assay(fcf, "zScore")
hist(zScore[,"ap_MESO_68h_1"], breaks=100)
hist(zScore[,"ap_MESO_68h_2"], breaks=100)
## ----zScoreDistribution2, eval=TRUE, cache=TRUE, fig.show='hold', dependson=c("zScoreDistribution")----
qqnorm(zScore[,"ap_MESO_68h_1"],
main="Normal Q-Q Plot - ap_MESO_68h_1")
abline(a=0, b=1)
qqnorm(zScore[,"ap_MESO_68h_2"],
main="Normal Q-Q Plot - ap_MESO_68h_2")
abline(a=0, b=1)
## ----addPeaks, eval=TRUE, cache=TRUE, fig.keep='none', dependson=c("CalculateZScores")----
fcf <- addPeaks(fcf, zScoreThresh=3, fdrThresh=0.01)
head(SummarizedExperiment::assay(fcf, "peaks"))
## ----fitDisplay, cache=TRUE, dependson=c("CalculateZScores"), fig.show='hold', fig.height=6, dev.args=list(pointsize=16)----
plotFits(fcf[,1], main="")
## ----plotZScores, eval=TRUE, cache=TRUE, fig.keep='all', fig.show='hold', dependson=c("CalculateZScores")----
library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
plotZScores(fcf[,c("ap_WE_68h_1", "ap_WE_68h_2")],
txdb=TxDb.Dmelanogaster.UCSC.dm3.ensGene)
## ----FindDifferences, eval=TRUE, cache=TRUE, dependson=c("CalculateZScores")----
fcf <- getDifferences(fcf,
referenceCondition="WE_68h")
fcf
## ----plotDispersion, cache=TRUE, dependson=c("FindDifferences"), dev.args=list(pointsize=16)----
plotDispEsts(fcf)
## ----normalizationFactors, cache=TRUE, dependson=c("FindDifferences"), dev.args=list(pointsize=16)----
plotNormalizationFactors(fcf)
## ----maplot, cache=TRUE, dependson=c("FindDifferences"), dev.args=list(pointsize=16)----
plotMA(results(fcf, contrast=c("condition", "WE_68h", "MESO_68h")),
alpha=0.01,
xlab="Mean 4C signal",
ylab="log2 fold change",
ylim=c(-3.1,3.1))
## ----results, cache=TRUE, dependson=c("FindDifferences")-------------------
results <- getAllResults(fcf)
dim(results)
head(results)[,1:6]
## ----plotDifferences, eval=TRUE, cache=TRUE, dependson=c("FindDifferences"), fig.height=10, fig.width=15, resize.width="0.9\\textwidth", dev.args=list(pointsize=12)----
plotDifferences(fcf,
txdb=TxDb.Dmelanogaster.UCSC.dm3.ensGene,
plotWindows = 1e+05,
textsize=16)
## ----integrationWithAnnotation1, eval=TRUE, cache=TRUE, fig.keep='none', dependson=c("FindDifferences")----
apId <- "FBgn0000099"
apGene <- genes(TxDb.Dmelanogaster.UCSC.dm3.ensGene,
filter=list(gene_id=apId))
apGene
## ----integrationWithAnnotation2, eval=TRUE, cache=TRUE, fig.keep='none', dependson=c("FindDifferences")----
apPromotor <- promoters(apGene, upstream = 500, downstream=100)
apPromotor
## ----integrationWithAnnotation3, eval=TRUE, cache=TRUE, fig.keep='none', dependson=c("FindDifferences")----
frags <- rowRanges(fcf)
if(length(frags) != nrow(results))
stop("Number of rows is not the same for the fragment data and results table.")
ov <- findOverlaps(apPromotor, frags)
ov
## ----integrationWithAnnotation4, eval=TRUE, cache=TRUE, fig.keep='none', dependson=c("FindDifferences")----
results[subjectHits(ov),1:6]
## ----sessionInfo-----------------------------------------------------------
sessionInfo()
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