tilingArray-package: tilingArray package overview
Description
tilingArray package overview
Details
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:
- The segmentation class
for representing partitionings of a linear series of data (such as
microarray intensity readings along a chromosome strand).
- The function
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).
- The function
plotAlongChrom for generating pretty
plots of segmentations along with genomic features. Please also see
the vignette Segmentation demo.
- The function
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).