computeOverlapFrequency: computeOverlapFrequency

Description Usage Arguments Value

View source: R/grangesProcessing.R

Description

This function compute the ('internal') overlapping frecuency of each feature (i.e. CNV) in a set. The overlap parameter sets the threshold to find out related CNVs. This approach takes the length of the GRanges object to compute the frequency value if totalCases parameter is NULL. It is recommendable to split the data by sequence name (chr) for huge GRange objects.

Usage

1
2
computeOverlapFrequency(granges, groupingVar = NULL, totalCases = NULL,
  overlap = 0.5)

Arguments

granges

granges object.

groupingVar

Not implemented.

totalCases

To normalized frequency values.

overlap

Only frequency for features overlaping above this threshold will be estimated, otherwise, this value will be zero.

Value

This function return a GRanges object keeping the initial information and two additional column with frequencies values.


enriquea/cnveR documentation built on May 13, 2017, 6:09 p.m.