xps (version 1.32.0)

firma: Finding Isoforms using Robust Multichip Analysis

Description

This function converts a DataTreeSet for exon arrays into an ExprTreeSet using the Finding Isoforms using Robust Multichip Analysis (FIRMA).

Usage

firma(xps.data, filename   = character(0), filedir    = getwd(), tmpdir     = "", background = "antigenomic", normalize  = TRUE, option     = "probeset", exonlevel  = "metacore", method     = "mdp", params     = list(16384, 0.0, 1.0, 10, 0.01, 1.0), xps.scheme = NULL, add.data   = TRUE, verbose    = TRUE)
xpsFIRMA(object, ...)

Arguments

xps.data

object of class DataTreeSet.

filename

file name of ROOT data file.

filedir

system directory where ROOT data file should be stored.

tmpdir

optional temporary directory where temporary ROOT files should be stored.

background

probes used to compute background, one of ‘genomic’, ‘antigenomic’

normalize

logical. If TRUE normalize data using quantile normalization.

option

option determining the grouping of probes for summarization, one of ‘exon’, ‘probeset’.

exonlevel

exon annotation level determining which probes should be used for summarization.

method

method to be used for summarization, currently ‘mdp’.

params

list of (default) parameters for rma.

xps.scheme

optional alternative SchemeTreeSet.

add.data

logical. If TRUE expression data will be included as slot data.

verbose

logical, if TRUE print status information.

object

object of class DataTreeSet.

...

the arguments described above.

Value

An ExprTreeSet

Details

This function computes FIRMA (Finding Isoforms using Robust Multichip Analysis) for detecting differential alternative splicing for exon arrays, as described in Purdom et al.

Following options are valid for exon arrays:

probeset:

expression levels are computed for individual probe sets, i.e. for each 'probeset_id'.

exon:

expression levels are computed for exon clusters, i.e. probe sets containing the same 'exon_id', where each exon cluster consists of one or more probesets.

Following exonlevel annotations are valid for exon arrays:

	core:
probesets supported by RefSeq and full-length GenBank transcripts.
metacore:	core meta-probesets.
	extended:
probesets with other cDNA support.
metaextended:	extended meta-probesets.
	full:
probesets supported by gene predictions only.
metafull:	full meta-probesets.
	ambiguous:
ambiguous probesets only.
affx:	standard AFFX controls.

Exon levels can also be combined, with following combinations being most useful:

exonlevel="metacore+affx":

core meta-probesets plus AFFX controls

exonlevel="core+extended":

probesets with cDNA support

exonlevel="core+extended+full":

supported plus predicted probesets

Exon level annotations are described in the Affymetrix whitepaper exon_probeset_trans_clust_whitepaper.pdf: “Exon Probeset Annotations and Transcript Cluster Groupings”.

Method xpsFIRMA is the DataTreeSet method called by function firma, containing the same parameters.

References

Purdom, E., Simpson K.M., Robinson M.D., Conboy J.G., Lapuk A.V. and Speed, T.P. (2008), FIRMA: a method for detection of alternative splicing from exon array data. Bioinformatics 24(15):1707-1714

Examples

## Not run: 
# ## load ROOT scheme file
# scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"
# scheme.exon <- root.scheme(paste(scmdir,"Scheme_HuEx10stv2r2_na27.root",sep="/"))
# 
# ## load subset of ROOT data file
# datdir <- "/Volumes/GigaDrive/CRAN/Workspaces/ROOTData"
# subnames <- c("HeartA","HeartB","HeartC", "MuscleA","MuscleB","MuscleC")
# sub.exon <- root.data(scheme.exon, rootFile(data.exon), celnames=subnames)
# 
# ## firma
# outdir <- getwd()
# sub.firma.ps <- firma(sub.exon,"HeartMuscleFIRMAcorePS",filedir=outdir,tmpdir="",background="antigenomic",
#                       normalize=TRUE,option="probeset",exonlevel="core")
# 
# ## get transcript expression levels for all transcripts or transcript=2429277
# expr.firma <- firma.expr(sub.firma.ps, probeset=NULL, option="transcript")
# expr.firma <- firma.expr(sub.firma.ps, probeset=2429277, option="transcript")
# 
# ## get probeset expression levels for all probeset or probeset=2429278 or transcript=2429277
# expr.firma <- firma.expr(sub.firma.ps, probeset=NULL, option="probeset")
# expr.firma <- firma.expr(sub.firma.ps, probeset=2429278, option="probeset")
# expr.firma <- firma.expr(sub.firma.ps, probeset=2429277, option="probeset")
# 
# ## get probeset splice scores for all probeset or probeset=2429278 or transcript=2429277
# score.firma <- firma.score(sub.firma.ps, probeset=NULL, option="probeset")
# score.firma <- firma.score(sub.firma.ps, probeset=2429278, option="probeset")
# score.firma <- firma.score(sub.firma.ps, probeset=2429277, option="probeset")
# 
# ## different plots
# boxplot(sub.firma.ps, which="UnitName:LEVEL_PS")
# boxplot(sub.firma.ps, which="UnitName:LEVEL_TS")
# 
# hist(sub.firma.ps, which="UnitName:LEVEL_PS")
# hist(sub.firma.ps, which="UnitName:LEVEL_TS")
# 
# rleplot(sub.firma.ps, which="UnitName:LEVEL_PS")
# rleplot(sub.firma.ps, which="UnitName:LEVEL_TS")
# 
# nuseplot(sub.firma.ps, which="UnitName:STDEV_PS")
# nuseplot(sub.firma.ps, which="UnitName:STDEV_TS")
# ## End(Not run)