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Convert genomic coordinates of peaks between genome assemblies

Source: R/weight.R
liftOverPeaks.Rd

This function converts genomic coordinates for a set of peaks to a specified genome assembly. The SCEGHiC package provides bulk average Hi-C data for the hg38 and mm10 assemblies, so coordinate conversion is required for other assemblies such as hg19 and mm9.

Usage

liftOverPeaks(split_peaks, genome)

Arguments

split_peaks

A matrix or data.frame with separated peak coordinates, typically obtained by splitting peak strings (e.g., "chr2-973888-974755") into columns for chromosome, start, and end.

genome

Character string specifying the genome assembly. Supported values are "hg19" or "mm9".

Value

A data.frame containing peaks after genome coordinate conversion, with updated chromosome, start, and end positions.

Examples

peaks <- c(
  "chr2-973888-974755", "chr2-3195868-3196264", "chr2-3242398-3243508", "chr2-6863856-6866834", "chr2-6913141-6914394",
  "chr2-6924663-6924972", "chr2-6999095-6999554", "chr2-7007713-7008819", "chr2-7083945-7084032", "chr2-7097148-7098029"
)
split_peaks <- do.call("rbind", strsplit(as.character(peaks), "-", fixed = TRUE))
peakinfo <- liftOverPeaks(split_peaks, "hg19")
head(peakinfo)
#>    chr   start     end                 peak  midpoint
#> 1 chr2  978202  979069   chr2_973888_974755  978635.5
#> 2 chr2 3192097 3192493 chr2_3195868_3196264 3192295.0
#> 3 chr2 3238627 3239737 chr2_3242398_3243508 3239182.0
#> 4 chr2 6723724 6726702 chr2_6863856_6866834 6725213.0
#> 5 chr2 6773010 6774263 chr2_6913141_6914394 6773636.5
#> 6 chr2 6784532 6784841 chr2_6924663_6924972 6784686.5