Description Usage Arguments Details Value References Examples
Calculate genomic region density
1 | genomicDensity(region, window.size = 1e7, n.window = NULL, overlap = TRUE)
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region |
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 |
Window size to calculate genomic density |
n.window |
number of windows, if it is specified, |
overlap |
Whether two neighbouring windows have half overlap |
It calculate the percent of each genomic windows that is covered by the input regions.
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.
Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.
1 2 3 | bed = generateRandomBed()
bed = subset(bed, chr == "chr1")
head(genomicDensity(bed))
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