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Genetic Variant Analysis

Find, analyze, and visualize genetic variants such as copy number variations (CNVs) and single nucleotide polymorphisms (SNPs)


cghcbsPerform circular binary segmentation (CBS) on array-based comparative genomic hybridization (aCGH) data
cghfreqplotDisplay frequency of DNA copy number alterations across multiple samples
chromosomeplotPlot chromosome ideogram with G-banding pattern
gcrmaPerform GC Robust Multi-array Average (GCRMA) background adjustment, quantile normalization, and median-polish summarization on Affymetrix microarray probe-level data
gcrmabackadjPerform GC Robust Multi-array Average (GCRMA) background adjustment on Affymetrix microarray probe-level data using sequence information
mattestPerform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes
mafdrEstimate false discovery rate (FDR) for multiple hypothesis testing
mavolcanoplotCreate significance versus gene expression ratio (fold change) scatter plot of microarray data
mairplotCreate intensity versus ratio scatter plot of microarray data
maboxplotCreate box plot for microarray data
maloglogCreate loglog plot of microarray data
mapcaplotCreate Principal Component Analysis (PCA) plot of microarray data
nbintestUnpaired hypothesis test for count data with small sample sizes


DataMatrixCreate DataMatrix object
DataMatrix objectData structure encapsulating data and metadata from microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers
NegativeBinomialTestUnpaired hypothesis test result


Detecting DNA Copy Number Alteration in Array-Based CGH Data

This example shows how to detect DNA copy number alterations in genome-wide array-based comparative genomic hybridization (CGH) data.

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