saasCNV (version 0.3.4)

Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data

Description

Perform joint segmentation on two signal dimensions derived from total read depth (intensity) and allele specific read depth (intensity) for whole genome sequencing (WGS), whole exome sequencing (WES) and SNP array data.

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Version

Install

install.packages('saasCNV')

Monthly Downloads

156

Version

0.3.4

License

GPL (>= 2)

Maintainer

Zhongyang Zhang

Last Published

May 18th, 2016

Functions in saasCNV (0.3.4)

vcf2txt

Covert VCF File to A Data Frame

internals

Internal Functions and Data

snp.cnv.data

Construct Data Frame for CNV Inference with SNP Array Data

cnv.data

Construct Data Frame for CNV Inference with NGS Data

cnv.call

CNV Calling from Sequencing Data

joint.segmentation

Joint Segmentation on log2ratio and log2mBAF Dimensions

reannotate.CNV.res

Gene Annotation

diagnosis.cluster.plot

Visualize Genome-Wide SCNA Profile in 2D Cluster Plot

snp.refine.boundary

Refine Segment Boundaries

NGS.CNV

CNV Analysis Pipeline for WGS and WES Data

saasCNV-package

Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data

genome.wide.plot

Visualize Genome-Wide SCNA Profile

merging.segments

Merge Adjacent Segments

diagnosis.seg.plot.chr

Visualize Segmentation Results for Diagnosis

GC.adjust

GC Content Adjustment

SNP.CNV

CNV Analysis Pipeline for SNP array Data