vcfR: peak_to_ploid – R documentation

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peak_to_ploid

Convert allele balance peaks to ploidy

Description

Converts allele balance data produced by freq_peak() to a copy number by assinging the allele balance data (frequencies) to its closest expected ratio.

Usage

peak_to_ploid(x)

Arguments

`x`	an object produced by `freq_peak()`.

Details

Converts allele balance data produced by freq_peak() to copy number. See the examples section for a graphical representation of the expectations and the bins around them. Once a copy number has called a distance from expectation (dfe) is calculated as a form of confidence. The bins around different copy numbers are of different width, so the dfe is scaled by its respective bin width. This results in a dfe that is 0 when it is exactly at our expectation (high confidence) and at 1 when it is half way between two expectations (low confidence).

Value

A list consisting of two matrices containing the calls and the distance from expectation (i.e., confidence).

Examples

# Thresholds.
plot(c(0.0, 1), c(0,1), type = "n", xaxt = "n", xlab = "Expectation", ylab = "Allele balance")
myCalls <-  c(1/5, 1/4, 1/3, 1/2, 2/3, 3/4, 4/5)
axis(side = 1, at = myCalls, labels = c('1/5', '1/4', '1/3','1/2', '2/3', '3/4', '4/5'), las=2)
abline(v=myCalls)
abline(v=c(7/40, 9/40, 7/24, 5/12), lty=3, col ="#B22222")
abline(v=c(7/12, 17/24, 31/40, 33/40), lty=3, col ="#B22222")
text(x=7/40, y=0.1, labels = "7/40", srt = 90)
text(x=9/40, y=0.1, labels = "9/40", srt = 90)
text(x=7/24, y=0.1, labels = "7/24", srt = 90)
text(x=5/12, y=0.1, labels = "5/12", srt = 90)
text(x=7/12, y=0.1, labels = "7/12", srt = 90)
text(x=17/24, y=0.1, labels = "17/24", srt = 90)
text(x=31/40, y=0.1, labels = "31/40", srt = 90)
text(x=33/40, y=0.1, labels = "33/40", srt = 90)

# Prepare data and visualize
data(vcfR_example)
gt <- extract.gt(vcf)
# Censor non-heterozygous positions.
hets <- is_het(gt)
is.na(vcf@gt[,-1][!hets]) <- TRUE
# Extract allele depths.
ad <- extract.gt(vcf, element = "AD")
ad1 <- masplit(ad, record = 1)
ad2 <- masplit(ad, record = 2)
freq1 <- ad1/(ad1+ad2)
freq2 <- ad2/(ad1+ad2)
myPeaks1 <- freq_peak(freq1, getPOS(vcf))
# Censor windows with fewer than 20 heterozygous positions
is.na(myPeaks1$peaks[myPeaks1$counts < 20]) <- TRUE
# Convert peaks to ploidy call
peak_to_ploid(myPeaks1)

vcfR

Manipulate and Visualize VCF Data

v1.12.0

GPL-3

Authors

Brian J. Knaus [cre, aut] (<https://orcid.org/0000-0003-1665-4343>), Niklaus J. Grunwald [aut] (<https://orcid.org/0000-0003-1656-7602>), Eric C. Anderson [ctb], David J. Winter [ctb], Zhian N. Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>), Javier F. Tabima [ctb] (<https://orcid.org/0000-0002-3603-2691>)

Initial release