tilingArray-package {tilingArray} | R Documentation |
tilingArray package overview
The package provides some functionalities that can be useful for the analysis of high-density tiling microarray data (such as Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are:
segment
for fitting piecewise constant models using a dynamic programming
algorithm that is both fast and exact,
and confint
for
calculating confidence intervals using the
strucchange package.
Please see the vignette Segmentation demo in the file
inst/doc/segmentation.pdf (source file inst/scripts/segmentation.Rnw).
plotAlongChrom
for generating pretty
plots of segmentations along with genomic features. Please also see
the vignette Segmentation demo.
normalizeByReference
for probe-sequence dependent response adjustment from
a (set of) reference hybridizations.
Please see the vignette Assessing signal/noise ratio before and after normalization in the file
inst/doc/assessNorm.pdf (source file inst/scripts/assessNorm.Rnw).
W. Huber <huber@ebi.ac.uk>