Calculate genomic region density
Calculate genomic region density
genomicDensity(
region,
window.size = 1e7,
n.window = NULL,
overlap = TRUE,
count_by = c("percent", "number"),
chr.len = NULL)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 |
count_by |
How to count the value for each window, |
chr.len |
the chromosome length. The value should be named vector |
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 the overlapping (value depends on the count_by argument). And if the input is a bed-format
data frame, there will be an additionally chromosome name column.
bed = generateRandomBed() bed = subset(bed, chr == "chr1") head(genomicDensity(bed)) head(genomicDensity(bed, count_by = "number"))
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