BACarray
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A package to analyze CGH arrays (2-color arrays) starting with raw data (.gpr files). Includes layout data from the FHCRC human BAC array.
Requires: R>1.80, BioConductor Package: DNAcopy.
Source: BACarray_0.6.tar.gz (right click to download)
PDF instructions: BACarray.pdf
What it does:
Source: BACarray_0.6.tar.gz (right click to download)
PDF instructions: BACarray.pdf
What it does:
• BAC.setup: Reads sample description file and sets arguments for BAC.norm function.
• BAC.norm: Reads raw data. Performs loess normalization. Writes normalized data to text file.
• BAC.ave: Reads normalized data. Averages spot replicates and sample replicates. Writes to text file.
• BAC.MvA.plot: Produces log-ratio vs. log-product (M vs A) plots and saves as a PDF file.
• BAC.chrom.seg: Perform DNA segment analysis on averaged data and outputs results to data file.
• BAC.chrom.plot: Plot data and segmentation results vs. chromosomal location. Outputs a PDF file.
NEW FEATURES!
• add.cytoband: Adds cytogenetic band locations which can be plotted with BAC.chrom.plot.
• plot.avg: Combines results from multiple samples into a single genome plot.
See also: FHCRC BAC array map files, GenePix Tips.
• BAC.norm: Reads raw data. Performs loess normalization. Writes normalized data to text file.
• BAC.ave: Reads normalized data. Averages spot replicates and sample replicates. Writes to text file.
• BAC.MvA.plot: Produces log-ratio vs. log-product (M vs A) plots and saves as a PDF file.
• BAC.chrom.seg: Perform DNA segment analysis on averaged data and outputs results to data file.
• BAC.chrom.plot: Plot data and segmentation results vs. chromosomal location. Outputs a PDF file.
NEW FEATURES!
• add.cytoband: Adds cytogenetic band locations which can be plotted with BAC.chrom.plot.
• plot.avg: Combines results from multiple samples into a single genome plot.
See also: FHCRC BAC array map files, GenePix Tips.
