doMCR {ADaCGH} | R Documentation |
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.
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, ...)
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). |
Used only for its side effects of writing out files.
Ramon Diaz-Uriarte rdiaz02@gmail.com
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.