TilePlot: Characterization of functional genes in complex microbial communities using tiling DNA microarrays

This package is intended for processing the output from functional gene tiling DNA microarray experiments. It produces hybridization pattern plots for each gene on the array, and statistics for each gene including mean probe intensity, median probe intensity, bright probe fraction, bright segment length dependent score, bright probe mean intensity, and bright probe median intensity. Output is generated in order of bright segment length dependent score in both a latex/eps format and tab-delimited text file. The package works in two modes: single array, and comparison of two arrays. Array comparison includes array comparison statistics: median of logarithm of one array probe divided by its counterpart on the other array, median absolute deviation of that value, and the binomial test to see whether the genes are equally abundant in both arrays.

AuthorIan Marshall
Date of publication2013-12-19 19:03:23
MaintainerIan Marshall <ianpgm@biology.au.dk>
LicenseGPL-2
Version1.3.1

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Files

TilePlot
TilePlot/inst
TilePlot/inst/allgenesonchip.ID
TilePlot/inst/all_annotations
TilePlot/inst/array1
TilePlot/inst/array2
TilePlot/NAMESPACE
TilePlot/R
TilePlot/R/tileplot.double.R TilePlot/R/tileplot.single.R TilePlot/R/compareplot.R TilePlot/R/TilePlot-internal.R
TilePlot/MD5
TilePlot/DESCRIPTION
TilePlot/man
TilePlot/man/tileplot.single.Rd TilePlot/man/compareplot.Rd TilePlot/man/tileplot.double.Rd TilePlot/man/TilePlot-package.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.