iterseg.genome.weighted: 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, iterative regression trees,and weighting to incentitze the regression to catch spikes.

Usage

iterseg.genome.weighted(
  df,
  png_filename,
  numiterations = 3,
  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	Specify a 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 (regtreepred)

Author(s)

Annika Cleven

Examples

example <- iterseg.genome.weighted(datafr127, png_filename = "datafr.png")
example$regtreepred
example$segments

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