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 positive false discovery rate 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 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 |