
Calculate genomic region density
genomicDensity(region, window.size = 1e7, n.window = NULL, overlap = TRUE)
Genomic positions. It can be a data frame with two columns which are start positions and end positions on a single chromosome. It can also be a bed-format data frame which contains the chromosome column.
Window size to calculate genomic density
number of windows, if it is specified, window.size
is ignored
Whether two neighbouring windows have half overlap
If the input is a two-column data frame, the function returns a data frame with three columns: start position, end position and percent of overlapping. And if the input is a bed-format data frame, there will be an additionally chromosome name column.
It calculate the percent of each genomic windows that is covered by the input regions.
Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.
# NOT RUN {
bed = generateRandomBed()
bed = subset(bed, chr == "chr1")
head(genomicDensity(bed))
# }
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