plotAltVsRef {DEploid.utils} | R Documentation |
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)
[Package DEploid.utils version 0.0.1 Index]