subclonesTumorCells: subclonesTumorCells Check the presence of subclonal...

In AntonioDeFalco/SCEVAN: SCEVAN

subclonesTumorCells Check the presence of subclonal structures in tumor cells, by determining the optimal number of clusters present in the CNA matrix of tumor cells using the Calinski-Harabasz Index as a criterion Calinski. For each possible subclone the joint segmentation algorithm is applied and the separate segmentation results are analyzed to see if there are any significant alterations specific to one subclone compared to the others.

Description

subclonesTumorCells Check the presence of subclonal structures in tumor cells, by determining the optimal number of clusters present in the CNA matrix of tumor cells using the Calinski-Harabasz Index as a criterion Calinski. For each possible subclone the joint segmentation algorithm is applied and the separate segmentation results are analyzed to see if there are any significant alterations specific to one subclone compared to the others.

Usage

subclonesTumorCells(
  tum_cells,
  CNAmat,
  relativeSmoothMtx,
  samp,
  n.cores,
  beta_vega
)

Arguments

tum_cells	malignant cells
CNAmat	CNA matrix
samp	sample name

Value

n_subclones number of subclones breaks_subclones breakpoints of subclones logCNA CNA matrix clustersSub clustering of subclones

AntonioDeFalco/SCEVAN documentation built on June 23, 2022, 11:08 a.m.