seg.chr: Segment and Visualize a Chromosome

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

Description

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

Usage

seg.chr(df, chromid)

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 id, for example "chr5"

Value

A list containing a dataframe with all of the segmentation data (segments), and a dataframe with the predictions from the regression tree (regtreepred), and a plot of the segmentation and chromosome data

Author(s)

Annika Cleven

Examples

example <- seg.chr(datafr, "chr5")
example$regtreepred
example$segments
example$plot

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