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Genetic Variant Analysis

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

Functions

cghcbs Perform circular binary segmentation (CBS) on array-based comparative genomic hybridization (aCGH) data
cghfreqplot Display frequency of DNA copy number alterations across multiple samples
chromosomeplot Plot chromosome ideogram with G-banding pattern
gcrma Perform GC Robust Multi-array Average (GCRMA) background adjustment, quantile normalization, and median-polish summarization on Affymetrix microarray probe-level data
gcrmabackadj Perform GC Robust Multi-array Average (GCRMA) background adjustment on Affymetrix microarray probe-level data using sequence information
mattest Perform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes
mafdr Estimate false discovery rate (FDR) for multiple hypothesis testing
mavolcanoplot Create significance versus gene expression ratio (fold change) scatter plot of microarray data
mairplot Create intensity versus ratio scatter plot of microarray data
maboxplot Create box plot for microarray data
maloglog Create loglog plot of microarray data
mapcaplot Create Principal Component Analysis (PCA) plot of microarray data
nbintest Unpaired hypothesis test for short-read count data with small sample sizes

Classes

DataMatrix Create DataMatrix object
DataMatrix object Data structure encapsulating data and metadata from microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers
NegativeBinomialTest Unpaired hypothesis test result

Topics

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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