Identification and genotyping of copy number variants using Illumina microarrays.

Documentation for package ‘CNstream’ version 1.0

CNstream-package	An R package for the identification and genotyping of copy number polymorphisms using Illumina microarrays.
CN.stream	CN.stream
CNstream	An R package for the identification and genotyping of copy number polymorphisms using Illumina microarrays.
cnv.findlimits	Given a 1D-GMM with N components, computes the intersection point between two components.
cnv.genotype	CNV analysis
cnv.gmm	Fits GMM model to the data and assigns CNV scores.
cnv.init	GMM initialization for CNV analysis
cnv.plot.gmm	Draws CNV models
emgmm.em	GMM Expectation-Maximization algorithm
emgmm.e_step	E-STEP GMM
emgmm.m_step	M-STEP GMM
emgmm.pdfgauss	GMM PDF EVALUATION
genotype.compute	SNP genotyping
genotype.findpeaks	Search for maxima over the histogram
genotype.marker	SNP genotyping
genotype.peaks	genotype.peaks
genotype.plot.pdf	Plots SNP genotype models
genotype.plot.result	SNP genotyping results plot
marker.analysis	Single-locus chi-square association test.
norm_gt	Intensity scaling
preprocessing	Plate normalization and channel intensity scaling
preprocessing.compute_fi	Coordinate transformation to B-allele frequency and absolute intensity
preprocessing.compute_inorm	Intensity scaling values
segment.analysis	Intensity scaling
segment.plot	Intensity scaling