DEploid (version 0.5.7)

reexports: Extract read counts from plain text file

Description

These objects are imported from other packages. Follow the links below to see their documentation.

DEploid.utils

computeObsWSAF, extractCoverageFromTxt, extractCoverageFromVcf, extractPLAF, haplotypePainter, histWSAF, plotAltVsRef, plotObsExpWSAF, plotProportions, plotWSAFvsPLAF

Value

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

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

A numeric array of PLAF

histogram

Numeric array of observed allele frequency within sample.

Arguments

refFileName

Path of the reference allele count file.

altFileName

Path of the alternative allele count file.

vcfFileName

Path of the VCF file.

ADFieldIndex

Index of the AD field of the sample field. For example, if the format is "GT:AD:DP:GQ:PL", the AD index is 2 (by default).

plafFileName

Path of the PLAF text file.

proportions

Matrix of the MCMC proportion samples. The matrix size is number of the MCMC samples by the number of strains.

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

exclusive

When TRUE 0 < WSAF < 1; otherwise 0 <= WSAF <= 1.

plaf

Numeric array of population level allele frequency.

potentialOutliers

Index of potential outliers.

obsWSAF

Numeric array of observed WSAF.

expWSAF

Numeric array of expected WSAF.

cex.lab

Label size.

cex.main

Title size.

cex.axis

Axis text size.

ref

Numeric array of reference allele count.

alt

Numeric array of alternative allele count.

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 inbreeding strains copying from.

See Also

histWSAF for histogram.

Examples

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

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

plafFile <- system.file("extdata", "labStrains.test.PLAF.txt",
  package = "DEploid"
)
plaf <- extractPLAF(plafFile)
if (FALSE) {
plafFile <- system.file("extdata", "labStrains.test.PLAF.txt",
  package = "DEploid"
)
panelFile <- system.file("extdata", "labStrains.test.panel.txt",
  package = "DEploid"
)
refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
PG0390CoverageT <- extractCoverageFromTxt(refFile, altFile)
PG0390Coverage.deconv <- dEploid(paste(
  "-ref", refFile, "-alt", altFile,
  "-plaf", plafFile, "-noPanel"
))
plotProportions(PG0390Coverage.deconv$Proportions, "PG0390-C proportions")
}

# 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)
plotAltVsRef(PG0390CoverageT$refCount, PG0390CoverageT$altCount)

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

# 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)
histWSAF(obsWSAF)
myhist <- histWSAF(obsWSAF, FALSE)

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

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


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"
)
PG0390.deconv <- dEploid(paste(
  "-vcf", vcfFile,
  "-plaf", plafFile, "-noPanel"
))
prop <- PG0390.deconv$Proportions[dim(PG0390.deconv$Proportions)[1], ]
expWSAF <- t(PG0390.deconv$Haps) %*% prop
plotObsExpWSAF(obsWSAF, expWSAF)

# 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)

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