saasCNV: Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data
Version 0.3.4

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.

Browse man pages Browse package API and functions Browse package files

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
URL https://zhangz05.u.hpc.mssm.edu/saasCNV/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("saasCNV")

Man pages

cnv.call: CNV Calling from Sequencing Data
cnv.data: Construct Data Frame for CNV Inference with NGS Data
diagnosis.cluster.plot: Visualize Genome-Wide SCNA Profile in 2D Cluster Plot
diagnosis.seg.plot.chr: Visualize Segmentation Results for Diagnosis
GC.adjust: GC Content Adjustment
genome.wide.plot: Visualize Genome-Wide SCNA Profile
internals: Internal Functions and Data
joint.segmentation: Joint Segmentation on log2ratio and log2mBAF Dimensions
merging.segments: Merge Adjacent Segments
NGS.CNV: CNV Analysis Pipeline for WGS and WES Data
reannotate.CNV.res: Gene Annotation
saasCNV-package: Somatic Copy Number Alteration Analysis Using Sequencing and...
SNP.CNV: CNV Analysis Pipeline for SNP array Data
snp.cnv.data: Construct Data Frame for CNV Inference with SNP Array Data
snp.refine.boundary: Refine Segment Boundaries
vcf2txt: Covert VCF File to A Data Frame

Functions

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

Files

inst
inst/doc
inst/doc/saasCNV.pdf
NAMESPACE
data
data/snp.segs.RData
data/snp.segs.merge.RData
data/snp.cnv.refine.anno.RData
data/seq.segs.merge.RData
data/seq.segs.RData
data/snp.cnv.anno.RData
data/seq.data.RData
data/snp.cnv.RData
data/snp.cnv.refine.RData
data/seq.cnv.RData
R
R/seg.summary.R
R/cnv.data.chr.R
R/BAF2mBAF.R
R/delta.sd.R
R/diagnosis.QQ.plot.R
R/msscan_tools.R
R/genome.wide.plot.R
R/check.overlap.R
R/vcf2txt.R
R/impute.missing.data.R
R/cnv.call.R
R/joint.segmentation.R
R/merging.segments.R
R/reannotate.CNV.res.R
R/compute.baseline.manual.R
R/compute.baseline.R
R/merging.segments.chr.R
R/diagnosis.cluster.plot.R
R/snp.refine.boundary.R
R/snp.cnv.data.R
R/GC.adjust.R
R/NGS.CNV.R
R/Mode.R
R/cnv.data.R
R/diagnosis.seg.plot.chr.R
R/SNP.CNV.R
MD5
DESCRIPTION
ChangeLog
man
man/NGS.CNV.Rd
man/GC.adjust.Rd
man/merging.segments.Rd
man/joint.segmentation.Rd
man/snp.refine.boundary.Rd
man/cnv.data.Rd
man/vcf2txt.Rd
man/cnv.call.Rd
man/SNP.CNV.Rd
man/saasCNV-package.Rd
man/internals.Rd
man/genome.wide.plot.Rd
man/snp.cnv.data.Rd
man/diagnosis.seg.plot.chr.Rd
man/diagnosis.cluster.plot.Rd
man/reannotate.CNV.res.Rd
saasCNV documentation built on May 19, 2017, 7:37 a.m.