importFromApt.CnChipEffectSet {aroma.affymetrix} | R Documentation |
Imports copy-number estimates from an APT summary file. Currently only total copy-number estimates can be imported.
CnChipEffectSet$importFromApt(filename, path=NULL, combineAlleles=TRUE, cdf, ..., skip=TRUE, verbose=FALSE)
filename |
The filename of the APT summary file. |
path |
An optional path to the file. |
combineAlleles |
If TRUE , ... |
cdf |
An AffymetrixCdfFile object. |
... |
Not used. |
skip |
If TRUE , already imported arrays will be skipped. |
verbose |
See Verbose . |
This import method is robust and memory efficient. One array at the time is imported by first writing to a temporary file which is then renamed to the final name, if import was successful. (If the import failed, a temporary file will rename that has to be deleted manually).
Since only one array at the time is imported, the memory overhead will be bounded allowing to import very large tab-delimited data files containing a large number of arrays. Unfortunately, this approach slows down the reading substantially, because in each import all but one column is parsed but ignored.
Returns an CnChipEffectSet
.
Henrik Bengtsson (http://www.braju.com/R/)
For more information see CnChipEffectSet
.