smoothRatio: A function to smooth ratio values using cubic smoothing...

In Repliscope: Replication Timing Profiling using DNA Copy Number

A function to smooth ratio values using cubic smoothing spline smoothRatio function splits values from 'ratio' column by chromosome and based the supplied 'groupMin' and 'split' parameters and then applies smooth.spline() function from R stats package. The supplied dataframe may contain multiple ratios, i.e. ratios produced using multiple replicating samples and/or multiple non-replicating samples. This must be reflected in 'name.rep' and 'name.nonRep' columns. In other words, different ratio dataframes may be merged using rbind() function before calling smoothRatio() function.

Description

A function to smooth ratio values using cubic smoothing spline smoothRatio function splits values from 'ratio' column by chromosome and based the supplied 'groupMin' and 'split' parameters and then applies smooth.spline() function from R stats package. The supplied dataframe may contain multiple ratios, i.e. ratios produced using multiple replicating samples and/or multiple non-replicating samples. This must be reflected in 'name.rep' and 'name.nonRep' columns. In other words, different ratio dataframes may be merged using rbind() function before calling smoothRatio() function.

Usage

smoothRatio(ratioDF, groupMin = 5, splitNum = 5)

Arguments

ratioDF	A ratio dataframe or combined ratios dataframe containing 'ratio' column (dataframe).
groupMin	Minimum number of values required to make a group (integer, defaults to 5).
splitNum	Minimum number of adjacent bins with missing values to close current group (integer, defaults to 5).

Examples

ratioDF <- smoothRatio(W303norm)

Repliscope documentation built on Sept. 13, 2022, 9:05 a.m.