inst/doc/SimFFPE.R

In SimFFPE: NGS Read Simulator for FFPE Tissue

### R code from vignette source 'SimFFPE.Rnw'

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### code chunk number 1: style
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BiocStyle::latex()


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### code chunk number 2: options
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options(width=60)


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### code chunk number 3: calcPhredScoreProfile
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library(SimFFPE)
bamFilePath <- system.file("extdata", "example.bam", package = "SimFFPE")
regionPath <- system.file("extdata", "regionsBam.txt", package = "SimFFPE")
regions <- read.table(regionPath)
PhredScoreProfile <- calcPhredScoreProfile(bamFilePath, targetRegions = regions)

## Example Phred score profile with 100 read length
PhredScoreProfilePath <- system.file("extdata", "PhredScoreProfile1.txt",
                                      package = "SimFFPE")
PhredScoreProfile <- as.matrix(read.table(PhredScoreProfilePath, skip = 1))
colnames(PhredScoreProfile) <- read.table(PhredScoreProfilePath, 
                                          nrows = 1, 
                                          colClasses = "character")
#
## Example Phred score profile with 150 read length

PhredScoreProfilePath2 <- system.file("extdata", "PhredScoreProfile2.txt",
                                      package = "SimFFPE")
PhredScoreProfile2 <- as.matrix(read.table(PhredScoreProfilePath2, skip = 1))
colnames(PhredScoreProfile2) <- read.table(PhredScoreProfilePath2, 
                                           nrows = 1, 
                                           colClasses = "character")



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### code chunk number 4: readDNAStringSet
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referencePath <- system.file("extdata", "example.fasta", package = "SimFFPE")
reference <- readDNAStringSet(referencePath)
reference



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### code chunk number 5: target region table
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regionPath <- system.file("extdata", "regionsSim.txt", package = "SimFFPE")
targetRegions <- read.table(regionPath)


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### code chunk number 6: readSimFFPE
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## Simulate reads of the first three sequences of the reference genome

sourceSeq <- reference[1:3]
outFile1 <- paste0(tempdir(), "/sim1")
readSimFFPE(sourceSeq, referencePath, PhredScoreProfile2, outFile1,
            overWrite = TRUE, coverage = 80, readLen = 150,
            enzymeCut = TRUE, threads = 4)
#
## Simulate reads of defined regions on the first two sequences of
## the reference genome

sourceSeq2 <- DNAStringSet(lapply(reference[1:2], function(x) x[1:10000]))
outFile2 <- paste0(tempdir(), "/sim2")
readSimFFPE(sourceSeq2, referencePath, PhredScoreProfile2, outFile2,
            overWrite = TRUE, coverage = 80, readLen = 150, enzymeCut = TRUE)



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### code chunk number 7: targetReadSimFFPE
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outFile3 <- paste0(tempdir(), "/sim3")
targetReadSimFFPE(referencePath, PhredScoreProfile, targetRegions, outFile3,
                  coverage = 120, readLen = 100, meanInsertLen = 180, 
                  sdInsertLen = 50, enzymeCut = FALSE)



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### code chunk number 8: sessionInfo
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packageDescription("SimFFPE")
sessionInfo()