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

In seasoncloud/Alleloscope: Allele-specific copy number genotyping for single cell sequencing data

HMM segmentation based on coverage matrix for paired tumor and normal sample.

Description

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

Usage

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 March 17, 2023, 1:14 a.m.