CNA.out: Shared CNA output

In FeiQin92/FLCNV: Simultaneous CNV Detection And Subclone Clustering With Single Cell Sequencing Data

Shared CNA output

Description

This function clusters the identified change-points to make final CNA calling. The potential CNA segments between two neighbor candidate change-points are assigned to different copy number states according to the estimated mean matrix from FLCNA R function. We use three clusters including duplication, normal state and deletion. A Gaussisan Mixture Model based clustering strategy was applied to assign each segment to the most likely cluster/state.

Usage

CNA.out(mean.matrix, LRR, Clusters, ref, cutoff = 0.4, L = 100)

Arguments

mean.matrix	The cluster mean matrix estimated from FLCNA R function.
cutoff	Cutoff value to further control the number of CNAs, the larger value of cutoff, the smaller number of CNAs. The default is 0.35.
L	Repeat times in the EM algorithm, defaults to 100.

Value

The return is the clustered CNA segments with start position, end position and copy number states.

state	The CNA states assigned.
start	The start point of CNAs.
end	The end point of CNAs.
chr	Chromosome of CNAs.
width	The width of CNAs.

FeiQin92/FLCNV documentation built on June 13, 2025, 3:30 a.m.