calcPhredScoreProfile: Estimate Phred score profile for FFPE read simulation
In SimFFPE: NGS Read Simulator for FFPE Tissue

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/param_estimator.R

Calculate Phred score profile from the entire BAM file or reads in subsampled regions.

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calcPhredScoreProfile(bamFilePath, mapqFilter = 0, maxFileSize = 1, 
targetRegions = NULL, subsampleRatio = NA, subsampleRegionLength = 1e+05, 
disableSubsampling = FALSE, threads = 1)

`bamFilePath`	BAM file to be processed.
`mapqFilter`	Filter for mapping quality. Reads with mapping quality below this value will be excluded from calculation.
`maxFileSize`	The maximum file size (in GB) that allows processing of the entire BAM file. If disableSubsampling is set to false, BAM file larger than this size will be subsampled for calculation.
`targetRegions`	A DataFrame or GenomicRanges object representing target regions for calculation. Use it for targeted sequencing / WES data, or when you need to manually select subsampled regions (set disableSubsampling to true in this case). If it is a DataFrame, the first column should be the chromosome, the second the start position and the third the end position. Please use one-based coordinate systems (the first base should be marked with 1 but not 0).
`subsampleRatio`	Subsample ratio. Together with subsampleRegionLength to determine subsampled regions. When subsampleRatio is not given, it will be assigned the value of maxFileSize divided by the input BAM file size. Range: 0 to 1.
`subsampleRegionLength`	Length of each subsampled region. Unit: base pair (bp).
`disableSubsampling`	Force to use the entire BAM file for calculation when set to true.
`threads`	Number of threads used. Multi-threading can speed up the process.

Calculate positional Phred score profile from the entire BAM file or reads in subsampled regions. A Phred score profile will be returned, which can then be used in read simulation.

A matrix will be returned. Each row of the matrix represents a position in the read (from begin to end), and each column the Phred quality score of base-calling error probabilities. The value in the matrix represents the positional Phred score proportion.

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

SimFFPE, readSimFFPE, targetReadSimFFPE

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)