treeInfo-methods: Get UserInfo from ROOT Trees

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

Description

Extract the UserInfo from ROOT trees, i.e. quality control information.

Usage

treeInfo(object, treename = "*", treetype = character(0), varlist = "*", qualopt = NULL, verbose = FALSE, ...)

Arguments

object	Object of class "TreeSet".
treename	Object of class "list" representing the names of the ROOT trees.
treetype	type of tree to export, see validTreetype
varlist	names of tree leaves to export.
qualopt	option determining the data to which to apply qualification, one of ‘raw’, ‘adjusted’, ‘normalized’, ‘all’.

Details

ROOT trees have a pointer to a list fUserInfo where it is possible to store data which do not fit into the usual tree structure. Taking advantage of this feature xps stores certain pre-processed results of the tree(s) in this list. For example, data trees store the minimal/maximal intensities and the number of oligos with minimal/maximal intensities of the CEL-files in list fUserInfo, while call trees store the number and percentage of P/M/A calls.

Function treeInfo allows to export this user information as a data.frame, whereby the parameters of varlist depend on the treetype:

Parameters for data trees with extensions "cel", "int", and background trees:
fMinInten: minimal intensity.
fMaxInten: maximal intensity.
fNMinInten: number of probes with minimal intensity.
fNMaxInten: number of probes with maximal intensity.
fMaxNPixels: maximal number of pixels.
fNQuantiles: number of precalculated quantiles.
fQuantiles: quantiles.
fIntenQuant: intensities at quantiles.

Parameters for expression trees:
fNUnits: number of units, i.e. probesets.
fMinLevel: minimal expression level.
fMaxLevel: maximal expression level.
fNQuantiles: number of precalculated quantiles.
fQuantiles: quantiles.
fLevelQuant: expression levels at quantiles.

Parameters for call trees:
fNUnits: number of units, i.e. probesets.
fNAbsent: number of units with absent call.
fNMarginal: number of units with marginal call.
fNPresent: number of units with present call.
fPcAbsent: percentage of units with absent call.
fPcMarginal: percentage of units with marginal call.
fPcPresent: percentage of units with present call.
fMinPValue: minimal p-value.
fMaxPValue: maximal p-value.

Parameters for border trees with extension "brd":
fMeanLeft: mean intensity of left border.
fMeanRight: mean intensity of right border.
fMeanTop: mean intensity of top border.
fMeanBottom: mean intensity of bottom border.
fCOIXhi: x-location of COI for the positive elements.
fCOIYhi: y-location of COI for the positive elements.
fCOIXlo: x-location of COI for the negative elements.
fCOIYlo: y-location of COI for the negative elements.

Parameters for quality trees with extension "rlm":
fNUnits: number of units, i.e. probesets.
fMinLevel: minimal expression level.
fMaxLevel: maximal expression level.
fNQuantiles: number of precalculated quantiles.
fQuantiles: quantiles.
fLevelQuant: expression levels at quantiles.
fNUSEQuant: NUSE at quantiles.
fRLEQuant: RLE at quantiles.
fQualOption: value of qualopt.

Parameters for residual trees with extension "res":
fNQuantiles: number of precalculated quantiles.
fQuantiles: quantiles.
fResiduQuant: residual at quantiles.
fWeightQuant: weight at quantiles.
fQualOption: value of qualopt.

Value

A data.frame.

Note

Taking advantage of function treeInfo plotting methods boxplot, callplot, coiplot, nuseplot and rleplot are able to display their results much faster, which is especially useful for large datasets.

Author(s)

Christian Stratowa

See Also

validTreetype

Examples

## load existing ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

userinfo <- treeInfo(data.test3, treetype="cel", varlist="*")
userinfo

userinfo <- treeInfo(data.test3, treename="TestB1", treetype="cel", varlist = "fNQuantiles:fIntenQuant")
userinfo

## Not run: 
userinfo <- treeInfo(rlm.all, treetype="rlm", varlist = "fNQuantiles:fNUSEQuant:fRLEQuant", qualopt = "raw")
userinfo

userinfo <- treeInfo(rlm.all, treetype="brd")
userinfo

userinfo <- treeInfo(rlm.all, treetype="res", qualopt = "raw")
userinfo

userinfo <- treeInfo(rlm.all, treetype="res", varlist = "fResiduQuant", qualopt = "raw")
userinfo

## End(Not run)

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