Package 'DEploid'

Deconvolute mixed haplotypes

Description

Deconvolute mixed haplotypes, and reporting the mixture proportions from each sample This function provieds an interface for calling dEploid from R. The command line options are passed via the args argument

Usage

dEploid(args)

Arguments

args	String of dEploid input.

Value

A list with members of haplotypes, proportions and log likelihood of the MCMC chain.

• Haps Haplotypes at the final iteration in plain text file.

• Proportions MCMC updates of the proportion estimates.

• llks Log likelihood of the MCMC chain.

Seeding

The R version of DEploid uses random number from R's random generator. Therefore, the '-seed' argument of the command line version will be ignored, and no seed is given in the output. Use the R function 'set.seed' prior to calling this function to ensure reproduciblity of results.

See Also

• vignette('dEploid-Arguments') for an overview of commandline arguments

Examples

## Not run: 
vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
set.seed(1234)
PG0390.deconv = dEploid(paste("-vcf", vcfFile, "-plaf", plafFile, "-noPanel"))

## End(Not run)

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Plot coverage

Description

Plot alternative allele count vs reference allele count at each site.

Usage

plotAltVsRefPlotly(ref, alt, title = "Alt vs Ref", potentialOutliers = c())

Arguments

ref	Numeric array of reference allele count.
alt	Numeric array of alternative allele count.
title	Figure title, "Alt vs Ref" by default
potentialOutliers	Index of potential outliers.

Examples

# Example 1
refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
PG0390CoverageT <- extractCoverageFromTxt(refFile, altFile)
plotAltVsRefPlotly(PG0390CoverageT$refCount, PG0390CoverageT$altCount)

# Example 2
vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
PG0390CoverageV <- extractCoverageFromVcf(vcfFile, "PG0390-C")
plotAltVsRefPlotly(PG0390CoverageV$refCount, PG0390CoverageV$altCount)

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WSAF histogram

Description

Produce histogram of the allele frequency within sample.

Usage

plotHistWSAFPlotly(obsWSAF, exclusive = TRUE, title = "Histogram 0<WSAF<1")

Arguments

obsWSAF	Observed allele frequency within sample
exclusive	When TRUE 0 < WSAF < 1; otherwise 0 <= WSAF <= 1.
title	Figure title, "Histogram 0<WSAF<1" by default

Value

histogram

Examples

# Example 1
refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
PG0390Coverage <- extractCoverageFromTxt(refFile, altFile)
obsWSAF <- computeObsWSAF(PG0390Coverage$altCount, PG0390Coverage$refCount)
plotHistWSAFPlotly(obsWSAF)
myhist <- plotHistWSAFPlotly(obsWSAF)

# Example 2
vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
PG0390CoverageV <- extractCoverageFromVcf(vcfFile, "PG0390-C")
obsWSAF <- computeObsWSAF(PG0390CoverageV$altCount, PG0390CoverageV$refCount)
plotHistWSAFPlotly(obsWSAF)
myhist <- plotHistWSAFPlotly(obsWSAF)

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Plot WSAF

Description

Plot observed alternative allele frequency within sample against expected WSAF.

Usage

plotObsExpWSAFPlotly(obsWSAF, expWSAF, title = "WSAF(observed vs expected)")

Arguments

obsWSAF	Numeric array of observed WSAF.
expWSAF	Numeric array of expected WSAF.
title	Figure title, "WSAF(observed vs expected)" by default

Examples

## Not run: 
vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
PG0390CoverageV <- extractCoverageFromVcf(vcfFile, "PG0390-C")
obsWSAF <- computeObsWSAF(PG0390CoverageV$altCount, PG0390CoverageV$refCount)
plafFile <- system.file("extdata", "labStrains.test.PLAF.txt",
  package = "DEploid"
)
PG0390CoverageV.deconv <- dEploid(paste(
  "-vcf", vcfFile,
  "-plaf", plafFile, "-noPanel"
))

prop <- PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv
$Proportions)[1], ]

expWSAF <- t(PG0390CoverageV.deconv$Haps) %*% prop
plotObsExpWSAFPlotly(obsWSAF, expWSAF)

## End(Not run)

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Plot WSAF vs PLAF

Description

Plot allele frequencies within sample against population level.

Usage

plotWSAFVsPLAFPlotly(
  plaf,
  obsWSAF,
  ref,
  alt,
  title = "WSAF vs PLAF",
  potentialOutliers = c()
)

Arguments

plaf	Numeric array of population level allele frequency.
obsWSAF	Numeric array of observed altenative allele frequencies within sample.
ref	Numeric array of reference allele count.
alt	Numeric array of alternative allele count.
title	Figure title, "WSAF vs PLAF" by default
potentialOutliers	Index of potential outliers.

Examples

# Example 1
refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
PG0390CoverageT <- extractCoverageFromTxt(refFile, altFile)
obsWSAF <- computeObsWSAF(PG0390CoverageT$altCount, PG0390CoverageT$refCount)
plafFile <- system.file("extdata", "labStrains.test.PLAF.txt",
  package = "DEploid"
)
plaf <- extractPLAF(plafFile)
plotWSAFVsPLAFPlotly(
  plaf, obsWSAF, PG0390CoverageT$refCount,
  PG0390CoverageT$altCount
)

# Example 2
vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
PG0390CoverageV <- extractCoverageFromVcf(vcfFile, "PG0390-C")
obsWSAF <- computeObsWSAF(PG0390CoverageV$altCount, PG0390CoverageV$refCount)
plafFile <- system.file("extdata", "labStrains.test.PLAF.txt",
  package = "DEploid"
)
plaf <- extractPLAF(plafFile)
plotWSAFVsPLAFPlotly(
  plaf, obsWSAF, PG0390CoverageV$refCount,
  PG0390CoverageV$altCount
)

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