summarize {xps} | R Documentation |
Converts Affymetrix probe level data to expression levels by summarizing the probe set values into one expression measure and a standard error for this summary.
summarize(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "none", method = character(), option = "transcript", logbase = "0", exonlevel = "", params = list(), xps.scheme = NULL, add.data = TRUE, verbose = TRUE) summarize.mas4(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, option = "transcript", exonlevel = "", xps.scheme = NULL, add.data = TRUE, verbose = TRUE) summarize.mas5(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, option = "transcript", exonlevel = "", xps.scheme = NULL, add.data = TRUE, verbose = TRUE) summarize.rma(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, option = "transcript", exonlevel = "", xps.scheme = NULL, add.data = TRUE, verbose = TRUE) xpsSummarize(object, ...)
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. |
update |
logical. If TRUE the existing ROOT data file filename will be updated. |
select |
type of probes to select for summarization. |
method |
summarization method to use. |
option |
option determining the grouping of probes for summarization, one of ‘transcript’, ‘exon’, ‘probeset’; exon arrays only. |
logbase |
logarithm base as character, one of ‘0’, ‘log’, ‘log2’, ‘log10’. |
exonlevel |
exon annotation level determining which probes should be used for summarization; exon/genome arrays only. |
params |
vector of parameters for summarization method. |
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. |
Converts Affymetrix probe level data to expression levels by summarizing the probe set values into one expression measure and a standard error for this summary.
xpsSummarize
is the DataTreeSet
method called by function summarize
,
containing the same parameters.
An ExprTreeSet
.
Christian Stratowa
## first, load 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="/")) ## RMA background data.bg.rma <- bgcorrect.rma(data.test3,"tmp_Test3RMA",filedir=getwd(),tmpdir="",verbose=FALSE) ## normalize quantiles data.qu.rma <- normalize.quantiles(data.bg.rma,"tmp_Test3RMA",filedir=getwd(),tmpdir="",update=TRUE,verbose=FALSE) ## summarize medianpolish data.mp.rma <- summarize.rma(data.qu.rma,"tmp_Test3RMA",filedir=getwd(),tmpdir="",update=TRUE,verbose=FALSE) ## get expression data.frame expr.rma <- exprs(data.mp.rma) head(expr.rma) ## plot expression levels if (interactive()) { boxplot(data.mp.rma) boxplot(log2(expr.rma[,3:6])) }