seg.genome: Segment and Visualize a Whole Genome

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

Description

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

Usage

seg.genome(df, png_filename, upper.y.lim = 5, lower.y.lim = -5, 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".
png_filename	A .png filename
upper.y.lim	The upper limit for the y value of the plot
lower.y.lim	The lower limit for the y value of the plot
cpvalue	Specified constant cp value for the regression tree to use instead of the optimal cp value

Value

A .png file with the whole genome plot and segmentation, a list containing a dataframe with all of the segmentation data(segments), and a dataframe with the predictions from the regression tree(regtreepred)

Author(s)

Annika Cleven

Examples

example <- seg.genome(datafr127, png_filename = "datafr.png",upper.y.lim = 5, lower.y.lim = -5)
example$regtreepred
example$segments

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