Description Usage Arguments Examples
Plot allele frequencies within sample against population level.
1 2 3 4 5 6 7 8 9 10 | plotWSAFvsPLAF(
plaf,
obsWSAF,
expWSAF = c(),
potentialOutliers = c(),
title = "WSAF vs PLAF",
cex.lab = 1,
cex.main = 1,
cex.axis = 1
)
|
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 |
Index of potential outliers. |
title |
Figure title, "WSAF vs PLAF" by default |
cex.lab |
Label size. |
cex.main |
Title size. |
cex.axis |
Axis text size. |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | # 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)
obsWSAF = computeObsWSAF(PG0390CoverageV$altCount, PG0390CoverageV$refCount)
plafFile = system.file("extdata", "labStrains.test.PLAF.txt",
package = "DEploid")
plaf = extractPLAF(plafFile)
plotWSAFvsPLAF(plaf, obsWSAF)
|
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