doMCR {ADaCGH}R Documentation

Find minimal common regions

Description

A wrapper for the functionality implemented in the cghMCR package suitable for objets such as those returned by our functions. Output is returned as HTML and text files.

Usage

doMCR(x, chrom.numeric, data, MCR.gapAllowed = 500,
      MCR.alteredLow = 0.03, MCR.alteredHigh = 0.97,
      MCR.recurrence = 75, fsink = "results.txt",
      hsink = "mcr.results.html", Pos, ...)

Arguments

x The "segm" component of an object returned by our pSegment* functions, such as pSegmentDNAcopy. For instance whatevername$semg, where whatevername is the result of a previous invocation of pSegment.
chrom.numeric See pSegmentDNAcopy
data The original aCGH data; genes in rows, subjects or arrays in columns. Data should be ordered by chromosome and position within chromosome.
MCR.gapAllowed See MCR
MCR.alteredLow See MCR
MCR.alteredHigh See MCR
MCR.recurrence See MCR
fsink Name of file where text results are written to.
hsink Name of file where HTML results are written to.
Pos The location (e.g., position in kbases) of each probe in the chromosome. A vector of the same length as the number of rows in data
... Additional arguments (not used now).

Value

Used only for its side effects of writing out files.

Author(s)

Ramon Diaz-Uriarte rdiaz02@gmail.com

References

Aguirre, Brennan, Bailey, Sinha, Feng, Leo, Zhang, Zhang, Gans, Bardeesy, Cauwels, Cordon-Cardo, Redston, Depinho, Chin. (2004). High-resolution characterization of the pancreatic adenocarcinoma genome. PNAS, 101: 9067–9072.

Diaz-Uriarte, R. and Rueda, O.M. (2006). ADaCGH: an R package and web-based application for the analysis of aCGH data. Tech. report. http://www.ligarto.org/rdiaz/Papers/adacgh.pdf, http://adacgh2.bioinfo.cnio.es.

See Also

MCR


[Package ADaCGH version 1.3-10 Index]