featureValue: Grabs a value for an interval that overlaps each breakpoint

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

Description

Grabs a value for an interval that overlaps each breakpoint

Usage

featureValue(query, feature, feature.name, column.name, 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 feature of interest.
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.
column.name	A character vector of length 1 specifying the name of the column in feature for which to grab a value from.
average	A logical (TRUE/FALSE) indicating whether or not to return the average value as well as the value for each individual breakpoint.

Examples

Example 1: Determining the replication timing score for each breakpoint
data(test_sv)
data(rep_timing)
featureValue(query = test_sv,
             feature = rep_timing,
             feature.name = 'repliscore',
             column.name = score,
             average = TRUE)

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