Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data

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Documentation for package ‘saasCNV’ version 0.3.4

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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