Genetic Variant Analysis
Find, analyze, and visualize genetic variants, such as copy number variations (CNVs) and single nucleotide polymorphisms (SNPs).
Functions
Circular Binary Segmentation
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 |
Normalization
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 |
Hypothesis Testing
Visualization
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 |
Objects
DataMatrix | Data structure encapsulating data and metadata from microarray experiment |
NegativeBinomialTest | Unpaired hypothesis test result |
Featured Examples
Detecting DNA Copy Number Alteration in Array-Based CGH Data
Detect DNA copy number alterations in genome-wide array-based comparative genomic hybridization (CGH) data.
Analyzing Affymetrix SNP Arrays for DNA Copy Number Variants
Study DNA copy number variants by preprocessing and analyzing data from the Affymetrix® GeneChip® Human Mapping 100k array.
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