SimFFPE-package: NGS Read Simulator for FFPE Tissue
In SimFFPE: NGS Read Simulator for FFPE Tissue

Description Details Author(s) See Also Examples

This package simulates artifact chimeric reads specifically generated in next-generation sequencing (NGS) process of formalin-fixed paraffin-embedded (FFPE) tissue.

This package was not yet installed at build time.
The NGS (Next-Generation Sequencing) reads from FFPE (Formalin-Fixed Paraffin-Embedded) samples contain numerous artificial chimeric reads. These reads are derived from the combination of two single-stranded DNA (ss-DNA) fragments with short reverse complementary sequences. The combined ss-DNA may come from adjacent or distant regions. This package simulates these artifacts as well as normal reads for FFPE samples. The simulation can cover whole genome, or several chromosomes, or large regions, or whole exome, or targeted regions. It also supports enzymatic / random fragmentation and paired-end / single-end sequencing simulations. Fine-tuning can be performed for desired simulation results, and multi-threading can help reduce the runtime. Please check the package vignette for the guidance of fine-tuning.

Index: This package was not yet installed at build time.
There are three available functions for NGS read simulation of FFPE samples:

1. calcPhredScoreProfile: Calculate positional Phred score profile from BAM file for read simulation.

2. readSimFFPE: Simulate noisy NGS reads of FFPE samples on whole genome, or several chromosomes, or large regions.

3. targetReadSimFFPE: Simulate noisy NGS reads of FFPE samples in exonic / targeted regions.

Lanying Wei

Maintainer: Lanying Wei <lanying.wei@uni-muenster.de>

calcPhredScoreProfile, readSimFFPE, targetReadSimFFPE

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

referencePath <- system.file("extdata", "example.fasta", package = "SimFFPE")
reference <- readDNAStringSet(referencePath)

## Simulate reads of the first three sequences of the reference genome

sourceSeq <- reference[1:3]
outFile1 <- paste0(tempdir(), "/sim1")
readSimFFPE(sourceSeq, referencePath, PhredScoreProfile, outFile1, 
            coverage = 80, enzymeCut = TRUE, threads = 4)

## Simulate reads for targeted regions

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)

regionPath <- system.file("extdata", "regionsSim.txt", package = "SimFFPE")
targetRegions <- read.table(regionPath)

outFile <- paste0(tempdir(), "/sim2")
targetReadSimFFPE(referencePath, PhredScoreProfile, targetRegions, outFile,
                  coverage = 120, readLen = 100, meanInsertLen = 150, 
                  sdInsertLen = 40, enzymeCut = FALSE)