importFromApt.CnChipEffectSet: Imports copy-number estimates from an APT summary file

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

Imports copy-number estimates from an APT summary file

Description

Imports copy-number estimates from an APT summary file. Currently only total copy-number estimates can be imported.

Usage

## Static method (use this):
## CnChipEffectSet$importFromApt(filename, path=NULL, combineAlleles=TRUE, cdf, ...,
##   skip=TRUE, verbose=FALSE)

## Don't use the below:
## S3 method for class 'CnChipEffectSet'
importFromApt(static, filename, path=NULL, combineAlleles=TRUE, cdf, ..., skip=TRUE,
  verbose=FALSE)

Arguments

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.

Details

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.

Value

Returns an CnChipEffectSet.

Author(s)

Henrik Bengtsson

See Also

For more information see CnChipEffectSet.

HenrikBengtsson/aroma.affymetrix documentation built on Feb. 20, 2024, 9:07 p.m.