Package 'DEploid.utils'

Compute observed WSAF

Description

Compute observed allele frequency within sample from the allele counts.

Usage

computeObsWSAF(alt, ref)

Arguments

alt	Numeric array of alternative allele count.
ref	Numeric array of reference allele count.

Value

Numeric array of observed allele frequency within sample.

See Also

histWSAF for histogram.

Examples

# Example 1
refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid.utils")
altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid.utils")
PG0390CoverageTxt <- extractCoverageFromTxt(refFile, altFile)
obsWSAF <- computeObsWSAF(PG0390CoverageTxt$altCount, PG0390CoverageTxt$refCount)

# Example 2
vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid.utils")
PG0390CoverageVcf <- extractCoverageFromVcf(vcfFile, "PG0390-C")
obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount)

---

Extract read counts from plain text file

Description

Extract read counts from tab-delimited text files of a single sample.

Usage

extractCoverageFromTxt(refFileName, altFileName)

Arguments

refFileName	Path of the reference allele count file.
altFileName	Path of the alternative allele count file.

Value

A data.frame contains four columns: chromosomes, positions, reference allele count, alternative allele count.

Note

The allele count files must be tab-delimited. The allele count files contain three columns: chromosomes, positions and allele count.

Examples

refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid.utils")
altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid.utils")
PG0390 <- extractCoverageFromTxt(refFile, altFile)

---

Extract VCF information

Description

Extract VCF information

Usage

extractCoverageFromVcf(filename, samplename)

Arguments

filename	VCF file name.
samplename	Sample name

Value

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

• CHROM SNP chromosomes.

• POS SNP positions.

• refCount reference allele count.

• altCount alternative allele count.

See Also

• extractCoverageFromVcf

• extractCoverageFromTxt

Examples

vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid.utils")
vcf = extractCoverageFromVcf(vcfFile, "PG0390-C")

---

Extract PLAF

Description

Extract population level allele frequency (PLAF) from text file.

Usage

extractPLAF(plafFileName)

Arguments

plafFileName

Path of the PLAF text file.

Value

A numeric array of PLAF

Note

The text file must have header, and population level allele frequency recorded in the "PLAF" field.

Examples

plafFile <- system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid.utils")
plaf <- extractPLAF(plafFile)

---

Painting haplotype according the reference panel

Description

Plot the posterior probabilities of a haplotype given the refernece panel.

Usage

haplotypePainter(
  posteriorProbabilities,
  title = "",
  labelScaling,
  numberOfInbreeding = 0
)

Arguments

posteriorProbabilities	Posterior probabilities matrix with the size of number of loci by the number of reference strain.
title	Figure title.
labelScaling	Scaling parameter for plotting.
numberOfInbreeding	Number of inbreading strains

Value

No return value called for side effects

---

WSAF histogram

Description

Produce histogram of the allele frequency within sample.

Usage

histWSAF(
  obsWSAF,
  exclusive = TRUE,
  title = "Histogram 0<WSAF<1",
  cex.lab = 1,
  cex.main = 1,
  cex.axis = 1
)

Arguments

obsWSAF	Observed allele frequency within sample
exclusive	When TRUE 0 < WSAF < 1; otherwise 0 <= WSAF <= 1.
title	Histogram title
cex.lab	Label size.
cex.main	Title size.
cex.axis	Axis text size.

Value

histogram

Examples

# Example 1
refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid.utils")
altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid.utils")
PG0390CoverageTxt <- extractCoverageFromTxt(refFile, altFile)
obsWSAF <- computeObsWSAF(PG0390CoverageTxt$altCount, PG0390CoverageTxt$refCount)
histWSAF(obsWSAF)
myhist <- histWSAF(obsWSAF, FALSE)

# Example 2
vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid.utils")
PG0390CoverageVcf <- extractCoverageFromVcf(vcfFile, "PG0390-C")
obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount)
histWSAF(obsWSAF)
myhist <- histWSAF(obsWSAF, FALSE)

---

Plot coverage

Description

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

Usage

plotAltVsRef(
  ref,
  alt,
  title = "Alt vs Ref",
  exclude.ref = c(),
  exclude.alt = c(),
  potentialOutliers = c(),
  cex.lab = 1,
  cex.main = 1,
  cex.axis = 1
)

Arguments

ref	Numeric array of reference allele count.
alt	Numeric array of alternative allele count.
title	Figure title, "Alt vs Ref" by default
exclude.ref	Numeric array of reference allele count at sites that are not deconvoluted.
exclude.alt	Numeric array of alternative allele count at sites that are not deconvoluted
potentialOutliers	Potential outliers
cex.lab	Label size.
cex.main	Title size.
cex.axis	Axis text size.

Value

No return value called for side effects

Examples

# Example 1
refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid.utils")
altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid.utils")
PG0390CoverageTxt <- extractCoverageFromTxt(refFile, altFile)
plotAltVsRef(PG0390CoverageTxt$refCount, PG0390CoverageTxt$altCount)

# Example 2
vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid.utils")
PG0390CoverageVcf <- extractCoverageFromVcf(vcfFile, "PG0390-C")
plotAltVsRef(PG0390CoverageVcf$refCount, PG0390CoverageVcf$altCount)

---

Plot WSAF

Description

Plot observed alternative allele frequency within sample against expected WSAF.

Usage

plotObsExpWSAF(
  obsWSAF,
  expWSAF,
  title = "WSAF(observed vs expected)",
  cex.lab = 1,
  cex.main = 1,
  cex.axis = 1
)

Arguments

obsWSAF	Numeric array of observed WSAF.
expWSAF	Numeric array of expected WSAF.
title	Figure title.
cex.lab	Label size.
cex.main	Title size.
cex.axis	Axis text size.

Value

No return value called for side effects

---

Plot proportions

Description

Plot the MCMC samples of the proportion, indexed by the MCMC chain.

Usage

plotProportions(
  proportions,
  title = "Components",
  cex.lab = 1,
  cex.main = 1,
  cex.axis = 1
)

Arguments

proportions	Matrix of the MCMC proportion samples. The matrix size is number of the MCMC samples by the number of strains.
title	Figure title.
cex.lab	Label size.
cex.main	Title size.
cex.axis	Axis text size.

Value

No return value called for side effects

---

Plot WSAF vs PLAF

Description

Plot allele frequencies within sample against population level.

Usage

plotWSAFvsPLAF(
  plaf,
  obsWSAF,
  expWSAF = c(),
  potentialOutliers = c(),
  title = "WSAF vs PLAF",
  cex.lab = 1,
  cex.main = 1,
  cex.axis = 1
)

Arguments

plaf	Numeric array of population level allele frequency.
obsWSAF	Numeric array of observed altenative allele frequencies within sample.
expWSAF	Numeric array of expected WSAF from model.
potentialOutliers	Potential outliers
title	Figure title, "WSAF vs PLAF" by default
cex.lab	Label size.
cex.main	Title size.
cex.axis	Axis text size.

Value

No return value called for side effects

Examples

# Example 1
refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid.utils")
altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid.utils")
PG0390CoverageTxt <- extractCoverageFromTxt(refFile, altFile)
obsWSAF <- computeObsWSAF(PG0390CoverageTxt$altCount, PG0390CoverageTxt$refCount)
plafFile <- system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid.utils")
plaf <- extractPLAF(plafFile)
plotWSAFvsPLAF(plaf, obsWSAF)

# Example 2
vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid.utils")
PG0390CoverageVcf <- extractCoverageFromVcf(vcfFile, "PG0390-C")
obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount)
plafFile <- system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid.utils")
plaf <- extractPLAF(plafFile)
plotWSAFvsPLAF(plaf, obsWSAF)

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