reexports: Extract read counts from plain text file

In DEploid: Deconvolute Mixed Genomes with Unknown Proportions

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

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.

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.

Note

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

The VCF file should only contain one sample. If more samples present in the VCF, it only returns coverage for of the first sample.

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

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)
## Not run: 
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")

## End(Not run)

# 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)

DEploid documentation built on April 4, 2025, 2:16 a.m.