Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data

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Documentation for package ‘saasCNV’ version 0.3.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

saasCNV-package	Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data
BAF2mBAF	Internal Functions and Data
check.overlap	Internal Functions and Data
cnv.call	CNV Calling from Sequencing Data
cnv.data	Construct Data Frame for CNV Inference with NGS Data
cnv.data.chr	Internal Functions and Data
compute.baseline	Internal Functions and Data
compute.baseline.manual	Internal Functions and Data
compute.var	Internal Functions and Data
computeBeta	Internal Functions and Data
computeMoments	Internal Functions and Data
computeTiltDirect	Internal Functions and Data
ComputeZ.fromS.R	Internal Functions and Data
ComputeZ.fromS.R.partial	Internal Functions and Data
computeZ.onechange	Internal Functions and Data
computeZ.onechange.sample	Internal Functions and Data
computeZ.squarewave.sample	Internal Functions and Data
dchi	Internal Functions and Data
delta.sd	Internal Functions and Data
diagnosis.cluster.plot	Visualize Genome-Wide SCNA Profile in 2D Cluster Plot
diagnosis.QQ.plot	Internal Functions and Data
diagnosis.seg.plot.chr	Visualize Segmentation Results for Diagnosis
fcompute.max.Z	Internal Functions and Data
fmscbs	Internal Functions and Data
fscan.max	Internal Functions and Data
GC.adjust	GC Content Adjustment
genome.wide.plot	Visualize Genome-Wide SCNA Profile
getCutoffMultisampleWeightedChisq	Internal Functions and Data
impute.missing.data	Internal Functions and Data
joint.segmentation	Joint Segmentation on log2ratio and log2mBAF Dimensions
matrix.max	Internal Functions and Data
merging.segments	Merge Adjacent Segments
merging.segments.chr	Internal Functions and Data
Mode	Internal Functions and Data
mscbs.classify	Internal Functions and Data
NGS.CNV	CNV Analysis Pipeline for WGS and WES Data
pmarg.sumweightedchisq	Internal Functions and Data
pvalueMultisampleWeightedChisq	Internal Functions and Data
reannotate.CNV.res	Gene Annotation
saasCNV	Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data
seg.summary	Internal Functions and Data
seq.cnv	Internal Functions and Data
seq.data	Internal Functions and Data
seq.segs	Internal Functions and Data
seq.segs.merge	Internal Functions and Data
SNP.CNV	CNV Analysis Pipeline for SNP array Data
snp.cnv	Internal Functions and Data
snp.cnv.anno	Internal Functions and Data
snp.cnv.data	Construct Data Frame for CNV Inference with SNP Array Data
snp.cnv.refine	Internal Functions and Data
snp.cnv.refine.anno	Internal Functions and Data
snp.data	Internal Functions and Data
snp.refine.boundary	Refine Segment Boundaries
snp.segs	Internal Functions and Data
snp.segs.merge	Internal Functions and Data
snp_table	Internal Functions and Data
vcf2txt	Covert VCF File to A Data Frame
vcf_table	Internal Functions and Data
vu	Internal Functions and Data