export.filter: Export filter data as text files

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Export data from classes FilterTreeSet or AnalysisTreeSet to outfile.

Usage

export.filter(xps.fltr, treename = "*", treetype = character(0), varlist = "*", outfile = character(0), sep = "\t", as.dataframe = FALSE, verbose = TRUE)

Arguments

xps.fltr	an object of type FilterTreeSet or AnalysisTreeSet.
treename	tree name to export.
treetype	type of tree(s) to export, 'pfr', 'ufr' or 'stt'.
varlist	names of tree leaves to export.
outfile	name of output file.
sep	column separator
as.dataframe	if TRUE a data.frame will be returned.
verbose	logical, if TRUE print status information.

Details

Export data from classes FilterTreeSet, or AnalysisTreeSet to outfile.

Parameter varlist lists the parameters to export:
- parameters are separated by ":", e.g. varlist="fUnitName:fFlag".
- for varlist="*" all valid parameters will be exported.

For class FilterTreeSet the following varlist parameters are valid:

	fUnitName:	unit name (probeset ID).
	fFlag:	mask.

For class AnalysisTreeSet varlist can contain annotation parameters and parameters of the resulting data.
Following varlist annotation parameters are valid:

	fUnitName:	unit name (probeset ID).
	fTranscriptID:	transcript\_id (probeset ID).
	fName:	gene name.
	fSymbol:	gene symbol.
	fAccession:	mRNA accession such as Refseq ID.
	fEntrezID:	entrez ID.
	fChromosome:	chromosome.
	fStart:	start position.
	fStop:	stop position.
	fStrand:	strand on chromosome.
	fCytoBand:	cytoband.

For class AnalysisTreeSet the following varlist parameters are valid:

	mn1:	mean of group 1.
	mn2:	mean of group 2.
	fc:	fold-change fc=mn2/mn1.
	se:	standard error.
	df:	degree of freedom.
	stat:	t-statistic.
	pval:	p-value.
	nper:	number of permutations.
	pcha:	p-chance.
	padj:	adjusted p-value.
	flag:	flag.
	mask:	only rows with flag=1 will be exported.

Value

If as.dataframe is TRUE, the data will be imported into the current R session as data.frame. Otherwise, NULL will be returned.

Author(s)

Christian Stratowa

See Also

export-methods

xps documentation built on Nov. 8, 2020, 6 p.m.