saasCNV: Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data

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.

Install the latest version of this package by entering the following in R:
install.packages("saasCNV")
AuthorZhongyang Zhang [aut, cre], Ke Hao [aut], Nancy R. Zhang [ctb]
Date of publication2016-05-18 02:04:56
MaintainerZhongyang Zhang <zhongyang.zhang@mssm.edu>
LicenseGPL (>= 2)
Version0.3.4
https://zhangz05.u.hpc.mssm.edu/saasCNV/

View on CRAN

Functions

BAF2mBAF Man page
check.overlap Man page
cnv.call Man page
cnv.data Man page
cnv.data.chr Man page
compute.baseline Man page
compute.baseline.manual Man page
computeBeta Man page
computeMoments Man page
computeTiltDirect Man page
compute.var Man page
ComputeZ.fromS.R Man page
ComputeZ.fromS.R.partial Man page
computeZ.onechange Man page
computeZ.onechange.sample Man page
computeZ.squarewave.sample Man page
dchi Man page
delta.sd Man page
diagnosis.cluster.plot Man page
diagnosis.QQ.plot Man page
diagnosis.seg.plot.chr Man page
fcompute.max.Z Man page
fmscbs Man page
fscan.max Man page
GC.adjust Man page
genome.wide.plot Man page
getCutoffMultisampleWeightedChisq Man page
impute.missing.data Man page
joint.segmentation Man page
matrix.max Man page
merging.segments Man page
merging.segments.chr Man page
Mode Man page
mscbs.classify Man page
NGS.CNV Man page
pmarg.sumweightedchisq Man page
pvalueMultisampleWeightedChisq Man page
reannotate.CNV.res Man page
saasCNV Man page
saasCNV-package Man page
seg.summary Man page
seq.cnv Man page
seq.data Man page
seq.segs Man page
seq.segs.merge Man page
snp.cnv Man page
SNP.CNV Man page
snp.cnv.anno Man page
snp.cnv.data Man page
snp.cnv.refine Man page
snp.cnv.refine.anno Man page
snp.data Man page
snp.refine.boundary Man page
snp.segs Man page
snp.segs.merge Man page
snp_table Man page
vcf2txt Man page
vcf_table Man page
vu Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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