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 |