Description Usage Arguments Details Value Author(s) See Also Examples
This function allows to combine different algorithms to compute background correction, normalization and fit a multichip model for summarization.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 | fitQC(xps.data,
filename = character(),
filedir = getwd(),
tmpdir = "",
update = FALSE,
# background correction
bgcorrect.method = "rma",
bgcorrect.select = "none",
bgcorrect.option = "pmonly:epanechnikov",
bgcorrect.params = c(16384),
# normalization
normalize.method = "quantile",
normalize.select = "pmonly",
normalize.option = "transcript:together:none",
normalize.logbase = "0",
normalize.params = c(0.0),
# quality control
qualify.method = "rlm",
qualify.select = "pmonly",
qualify.qualopt = "all",
qualify.option = "transcript",
qualify.estimator = "huber",
qualify.logbase = "log2",
qualify.params = list(10, 0.01, 1.0),
# reference values
reference.index = 0,
reference.method = "mean",
reference.params = list(0.0),
# misc.
exonlevel = "",
xps.scheme = NULL,
add.data = FALSE,
bufsize = 32000,
verbose = TRUE)
xpsQualityControl(object, ...)
|
xps.data |
object of class |
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 |
bgcorrect.method |
background method to use. |
bgcorrect.select |
type of probes to select for background correction. |
bgcorrect.option |
type of background correction to use. |
bgcorrect.params |
vector of parameters for background method. |
normalize.method |
normalization method to use. |
normalize.select |
type of probes to select for normalization. |
normalize.option |
normalization option. |
normalize.logbase |
logarithm base as character, one of ‘0’, ‘log’, ‘log2’, ‘log10’. |
normalize.params |
vector of parameters for normalization method. |
qualify.method |
qualification method to use, currently |
qualify.select |
type of probes to select for qualification. |
qualify.qualopt |
option determining the data to which to apply qualification, one of ‘raw’, ‘adjusted’, ‘normalized’, ‘all’. |
qualify.option |
option determining the grouping of probes for qualification, one of ‘transcript’, ‘exon’, ‘probeset’; exon arrays only. |
qualify.estimator |
option determining the M-estimator to use, one of ‘huber’, ‘fair’, ‘cauchy’, ‘gemanmcclure’, ‘welsch’, ‘tukey’, ‘andrew’. |
qualify.logbase |
logarithm base as character, one of ‘0’, ‘log’, ‘log2’, ‘log10’. |
qualify.params |
vector of parameters for qualification method. |
reference.index |
index of reference tree to use, or 0. |
reference.method |
for |
reference.params |
vector of parameters for reference method. |
exonlevel |
exon annotation level determining which probes should be used for summarization; exon/genome arrays only. |
xps.scheme |
optional alternative |
add.data |
logical. If |
bufsize |
integer which sets the buffer size of the tree branch baskets (default is 32000). |
verbose |
logical, if |
object |
object of class |
... |
the arguments described above. |
This function allows to combine different algorithms to compute background correction, normalization and fit a multichip model for summarization.
xpsQualityControl
is the DataTreeSet
method called by function fitQC
,
containing the same parameters.
An object of type QualTreeSet
.
Christian Stratowa
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | ## Not run:
## 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="/"))
## qualification - rlm
rlm.all <- fitQC(data.test3, "tmp_Test3RLMall", filedir=getwd(), tmpdir="",
qualify.method="rlm", qualify.qualopt="all", qualify.option="transcript", add.data=FALSE)
## get expression data.frame
expr.rlm.all <- validData(rlm.all)
## get borders
brd.rlm.all <- borders(rlm.all)
## get residuals
res.rlm.all <- residuals(rlm.all)
## get weights
w.rlm.all <- weights(rlm.all)
## plot expression levels
if (interactive()) {
coiplot(rlm.all)
borderplot(rlm.all)
nuseplot(rlm.all)
rleplot(rlm.all)
image(rlm.all, type="resids")
}
## End(Not run)
|
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