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

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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.

Author
Zhongyang Zhang [aut, cre], Ke Hao [aut], Nancy R. Zhang [ctb]
Date of publication
2016-05-18 02:04:56
Maintainer
Zhongyang Zhang <zhongyang.zhang@mssm.edu>
License
GPL (>= 2)
Version
0.3.4
URLs

View on CRAN

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

Files in this package

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