rePOS: Create non-overlapping positions (POS) for VCF data

In vcfR: Manipulate and Visualize VCF Data

Create non-overlapping positions (POS) for VCF data

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

rePOS(x, lens, ret.lens = FALSE, buff = 0)

Arguments

x	a vcfR object
lens	a data.frame describing the reference
ret.lens	logical specifying whether lens should be returned
buff	an integer indicating buffer length

Details

Each chromosome in a genome typically begins with position one. This creates a problem when plotting the data associated with each chromosome because the information will overlap. This function uses the information in the data.frame lens to create a new coordinate system where chromosomes do not overlap.

The data.frame lens should have a row for each chromosome and two columns. The first column is the name of each chromosome as it appears in the vcfR object. The second column is the length of each chromosome.

The parameter buff indicates the length of a buffer to put in between each chromosome. This buffer may help distinguish chromosomes from one another.

In order to create the new coordinates the lens data.frame is updated with the new start positions. The parameter

Value

Either a vector of integers that represent the new coordinate system or a list containing the vector of integers and the lens data.frame.

Examples

# Create some VCF data.
data(vcfR_example)
vcf1 <-vcf[1:500,]
vcf2 <-vcf[500:1500,]
vcf3 <- vcf[1500:2533]
vcf1@fix[,'CHROM'] <- 'chrom1'
vcf2@fix[,'CHROM'] <- 'chrom2'
vcf3@fix[,'CHROM'] <- 'chrom3'
vcf2@fix[,'POS'] <- as.character(getPOS(vcf2) - 21900)
vcf3@fix[,'POS'] <- as.character(getPOS(vcf3) - 67900)
vcf <- rbind2(vcf1, vcf2)
vcf <- rbind2(vcf, vcf3)
rm(vcf1, vcf2, vcf3)

# Create lens
lens <- data.frame(matrix(nrow=3, ncol=2))
lens[1,1] <- 'chrom1'
lens[2,1] <- 'chrom2'
lens[3,1] <- 'chrom3'
lens[1,2] <- 22000
lens[2,2] <- 47000
lens[3,2] <- 32089

# Illustrate the issue.
dp <- extract.info(vcf, element="DP", as.numeric=TRUE)
plot(getPOS(vcf), dp, col=as.factor(getCHROM(vcf)))

# Resolve the issue.
newPOS <- rePOS(vcf, lens)
dp <- extract.info(vcf, element="DP", as.numeric=TRUE)
plot(newPOS, dp, col=as.factor(getCHROM(vcf)))

# Illustrate the buffer
newPOS <- rePOS(vcf, lens, buff=10000)
dp <- extract.info(vcf, element="DP", as.numeric=TRUE)
plot(newPOS, dp, col=as.factor(getCHROM(vcf)))

vcfR documentation built on Feb. 16, 2023, 8:12 p.m.