iterseg.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 and iterative regression trees.

Usage

iterseg.genome(
  df,
  png_filename,
  cpvalue = NA,
  upper.y.lim = 5,
  lower.y.lim = 5
)

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
cpvalue	Specified constant cp value for the regression tree to use instead of the optimal cp value
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

Value

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

Author(s)

Annika Cleven

Examples

example <- iterseg.genome(s131L001, "example.png")
example$regtreepred
example$segments

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