iterseg.chr: Segment and Visualize a Single Chromosome

In annikacleven/regtreesegpackage: Segmenting CNV and BAF data using regression tree methods

Description

Creates a plot of the chromosome of interest segmented, a dataframe including all the segments, and a dataframe including the predictions from the regression tree using the optimal cp value for the chromosome, and iterative regression trees.

Usage

iterseg.chr(df, chromid, cpvalue = NA)

Arguments

df	A dataframe with columns of Start.Pos, log2r, and Chr columns. The Chr column should have format like "chr1", "chr21", "chrY".
chromid	The chromosome of interest in the form "chr3" or "chr21"
cpvalue	Specify a constant cp value for the regression tree to use instead of the optimal cp value

Value

A list containing a dataframe with all of the segmentation data (segments), and a dataframe with the predictions from the regression tree (regtreepred), a plot of the chromosome data and final predictions (chrplot), a list 5 plots of each step in iteration (plots)

Author(s)

Annika Cleven

Examples

example <- iterseg.chr(dataframe, "example.png")
example$regtreepred
example$segments
example$plots$iter2

annikacleven/regtreesegpackage documentation built on Dec. 19, 2021, 3:40 a.m.