breakpointGC: Determines the GC content surrounding structural variant...

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

Description

Determines the GC content surrounding structural variant breakpoints

Usage

breakpointGC(query, padding, average)

Arguments

query	A GRanges object containing breakpoint 1 with a GRanges for breakpoint 2 in a metadata column caled linked.to
padding	A character vector of length 1 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 "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 GC content near the two breakpoints for each structural variant

Examples

Example 1: Determining the GC content of 1kb, and 10kb surrounding each breakpoint and computing the average
           for each structural variant and each distance.
data(test_sv)
breakpointGC(query = test_sv, padding = "1kb", average = TRUE)

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