Segmentation: HMM segmentation based on coverage matrix for paired tumor...

Description Usage Arguments Value

View source: R/Segmentation.R

Description

If there is no paired normal, other normal sample with the same genome coordinate also works.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
Segmentation(
  Obj_filtered = NULL,
  raw_counts = NULL,
  ref_counts = NULL,
  hmm_states = c(0.5, 1.5, 1.8),
  hmm_sd = 0.2,
  hmm_p = 1e-06,
  nmean = 100,
  plot_seg = TRUE,
  rds_path = NULL,
  adj = 0,
  max_qt = 0.99
)

Arguments

Obj_filtered

An Alleloscope object.

raw_counts

A binned coverage matrix (m1 bin by n1 cell) with values being read counts in DNA sequencing data for all chromosomal regions of tumor sample. n1 can be 1 for bulk sample.

ref_counts

A binned coverage matrix (m2 bin by n2 cell) with values being read counts in DNA sequencing data for all chromosomal regions of normal sample. n2 can be 1 for bulk sample. Numbers of bins (rows) should be the same in the paired chromosomal regions for the paired samples

hmm_states

An ordered vector for the HMM numeric states (deletion, 1-copy gain, 2-copy gains).

hmm_sd

Numeric. Fixed standard deviation for the HMM states.

hmm_p

Numeric. Transition probability for the HMM algorithm.

nmean

Integer. Width of moving window for runmean.

plot_seg

Logical (TRUE/ FALSE). Whether or not to plot the segmentation result.

rds_path

The path for saving the rds files for the estimated results for each region.

adj

Numeric. Value for tumor coverage adjustment.

max_qt

Numeric value in 0,1. Setting the maximum value to the max_qt quantile to avoid extreme values.

Value

A Alleloscope object with "seg_table" added.


seasoncloud/Alleloscope documentation built on Feb. 21, 2022, 9:57 a.m.