Help for package DEploid

Type:

Package

Title:

Deconvolute Mixed Genomes with Unknown Proportions

Version:

0.5.7

Description:

Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haplotype searches in a multiple infection setting. This package is primarily developed as part of the Pf3k project, which is a global collaboration using the latest sequencing technologies to provide a high-resolution view of natural variation in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from patient blood sample, which often contains more than one parasite strain, with unknown proportions. This package is used for deconvoluting mixed haplotypes, and reporting the mixture proportions from each sample.

URL:

https://github.com/DEploid-dev/DEploid-r

BugReports:

https://github.com/DEploid-dev/DEploid-r/issues

License:

GPL (≥ 3)

Depends:

R (≥ 3.1.0), DEploid.utils (≥ 0.0.1)

Imports:

Rcpp (≥ 0.11.2), scales (≥ 0.4.0), plotly (≥ 4.7.1), magrittr (≥ 1.5), rmarkdown(≥ 1.6), htmlwidgets (≥ 1.0)

Suggests:

knitr, testthat (≥ 0.9.0)

VignetteBuilder:

knitr

LinkingTo:

Rcpp

RoxygenNote:

7.3.2

Encoding:

UTF-8

Date:

2024-12-22

NeedsCompilation:

yes

Packaged:

2025-01-20 02:29:18 UTC; rstudio

Author:

Joe Zhu

[aut, cre], Jacob Almagro-Garcia [aut], Gil McVean [aut], University of Oxford [cph], Yinghan Liu [ctb], CodeCogs Zyba Ltd [com, cph], Deepak Bandyopadhyay [com, cph], Lutz Kettner [com, cph]

Maintainer:

Joe Zhu <sha.joe.zhu@gmail.com>

Repository:

CRAN

Date/Publication:

2025-01-20 03:20:02 UTC

DEploid: Deconvolute Mixed Genomes with Unknown Proportions

Description

Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haplotype searches in a multiple infection setting. This package is primarily developed as part of #' the Pf3k project, which is a global collaboration using the latest sequencing technologies to provide a high-resolution view of natural variation in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from patient blood sample, which often contains more than one parasite strain, with unknown proportions. This package is used for deconvoluting mixed haplotypes, #' and reporting the mixture proportions from each sample.

Author(s)

Maintainer: Joe Zhu sha.joe.zhu@gmail.com (ORCID)

Authors:

Jacob Almagro-Garcia
Gil McVean

Other contributors:

University of Oxford [copyright holder]
Yinghan Liu [contributor]
CodeCogs Zyba Ltd [compiler, copyright holder]
Deepak Bandyopadhyay [compiler, copyright holder]
Lutz Kettner [compiler, copyright holder]

Zhu Sha

Maintainer: Joe Zhu sha.joe.zhu@gmail.com

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.

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)

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)

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)

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)

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
)

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 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.

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: Deconvolute Mixed Genomes with Unknown Proportions

Description

Author(s)

See Also

Deconvolute mixed haplotypes

Description

Usage

Arguments

Value

Seeding

See Also

Examples

Plot coverage

Description

Usage

Arguments

Examples

WSAF histogram

Description

Usage

Arguments

Value

Examples

Plot WSAF

Description

Usage

Arguments

Examples

Plot WSAF vs PLAF

Description

Usage

Arguments

Examples

Extract read counts from plain text file

Description

Arguments

Value

Note

See Also

Examples