segment: Recursive segmentation algorithm for CNV detection and...

In CODEX: A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing

Description

Recursive segmentation algorithm for CNV detection and genotyping, using normalized read depth from whole exome sequencing.

Usage

segment(Y_qc, Yhat, optK, K, sampname_qc, ref_qc, chr, lmax, mode)

Arguments

Y_qc	Raw read depth matrix after quality control procedure returned from qc
Yhat	Normalized read depth matrix returned from normalize
optK	Optimal value K returned from choiceofK
K	Number of latent Poisson factors. Can be an integer if optimal solution has been chosen or a vector of integers so that AIC, BIC, and RSS are computed for choice of optimal k.
sampname_qc	Vector of sample names after quality control procedure returned from qc
ref_qc	IRanges object of genomic positions of each exon after quality control procedure returned from qc
chr	Chromosome number returned from getbambed
lmax	Maximum CNV length in number of exons returned.
mode	Can be either "integer" or "fraction", which respectively correspond to format of the returned copy numbers.

Value

Final callset of CNVs with genotyping results.

Author(s)

Yuchao Jiang [e-mail]

See Also

normalize, choiceofK

Examples

Y_qc <- qcObjDemo$Y_qc
Yhat <- normObjDemo$Yhat
BIC <- normObjDemo$BIC
K <- normObjDemo$K
sampname_qc <- qcObjDemo$sampname_qc
ref_qc <- qcObjDemo$ref_qc
chr <- bambedObjDemo$chr
finalcall <- segment(Y_qc, Yhat, optK = K[which.max(BIC)], K = K, sampname_qc,
    ref_qc, chr, lmax = 200, mode = "integer")
finalcall

CODEX documentation built on Nov. 8, 2020, 8:22 p.m.