featureDensity: Determines the density of genomic features surrounding...

In cancer-genomics/plasmasv: Methods for identification of tumor-specific structural variants in plasma

Description

Determines the density of genomic features surrounding breakpoints

Usage

featureDensity(query, feature, feature.name, padding, average)

Arguments

query	A GRanges object containing breakpoint 1 with a GRanges for breakpoint 2 in a metadata column caled linked.to
feature	A GRanges object containing the features to compute the density from
feature.name	A character vector of length 1 indicating the name of the feature being evaluated. This value is only used to create the output table.
padding	A character vector containing the padding to be added to the positions in subject. Breakpoints in subject that overlap a breakpoint for an element in query +/- padding will be counted as an overlap for that element of query. Example values are "100bp", "1kb", 5mb", etc., where internally kb is coerced to '000' and mb is coerced to '000000'.
average	A logical (TRUE/FALSE) indicating whether or not to return the average value as well as the value for each individual breakpoint.

Details

Computes the fraction of basepairs within query +/- padding that are within feature

Examples

Example 1: Determining the fraction of bases in query +/- 500kb for in each structural variant in test_sv that
are in protein-coding gene regions
data(test_sv)
data(gene)
featureDensity(query = test_sv, feature = gene, feature.name = "gene", padding = "500kb", average = TRUE)

cancer-genomics/plasmasv documentation built on May 15, 2020, 11:35 a.m.