scaledCoverage: Help function for calculation of scaled junction coverages

In csoneson/jcc: Calculate JCC Scores

Help function for calculation of scaled junction coverages

Description

Function to calculate the scaled junction coverages for a given gene

Usage

scaledCoverage(uniqreads, mmreads, predcovs, g, beta = 1, ...)

Arguments

uniqreads	Vector with the number of uniquely mapping junction-spanning reads for each junction in the gene.
mmreads	Vector with the number of multimapping junction-spanning reads for each junction in the gene.
predcovs	Vector with the predicted junction coverages for each junction in the gene.
g	Junction weight function that takes as input the fraction of uniquely mapping reads for the junction, and returns a weight for the junction contribution to the score.
beta	Scaling exponent. If beta=1, predicted coverages are scaled to have the same (weighted) sum as the observed coverages. If beta=0, no scaling is done.
...	Additional parameters passed to g.

Value

A vector of scaled junction coverages

Author(s)

Charlotte Soneson

csoneson/jcc documentation built on July 18, 2024, 2:29 a.m.