"FCSmetadata-class" {rflowcyt} | R Documentation |
Information from the HEADER and TEXT of a raw binary FCS file about the data and other parameters are stored in the metadata.
Objects can be created by calls of the form new("FCSmetadata", ...)
.
mode
:"character"
the "$MODE" mode of
the raw binary FCS filesize
:"numeric"
the "$TOT" row
dimension of the data; describing the number of observations or
cells nparam
:"numeric"
the "$PAR" column
dimension of the data; describing the number of parameters shortnames
:"vector"
the "$PnN"
short names corresponding to the column variables of the data; these
names are generally non-descript and are not used as the names of the
columns of the datalongnames
:"vector"
the "$PnS"
long names used for the column variables of the dataparamranges
:"vector"
the
"$PnR" maximum value corresponding to the column variablesfilename
:"character"
path and/or
name of the original raw binary FCS object objectname
:"character"
the
name of the original, FCS-class
objectoriginal
:"logical"
the
original status of the current object fcsinfo
:"list"
the other
parameters and values in the HEADER and TEXT of the raw binary FCS
file signature(x = "FCSmetadata")
: Extracts the metadata
slots or metadata@fcsinfo slots by using a single character name
index; Extracts the metadata@fcsinfo slots by using a single or
vector of numerical indicies signature(x = "FCSmetadata")
: Replaces the metadata
slots or metadata@fcsinfo slots by using a single character name
index; Replaces the metadata@fcsinfo slots by using a single or
vector of numerical indicies;Adds a new slot to the
metadata@fcsinfo signature(x = "FCSmetadata")
: Extracts the metadata
slots or metadata@fcsinfo slots by using a single character name
index; Extracts the metadata@fcsinfo slots by using a single or
vector of numerical indicies signature(x = "FCSmetadata")
: Replaces the metadata
slots or metadata@fcsinfo slots by using a single character name
index; Replaces the metadata@fcsinfo slots by using a single or
vector of numerical indicies;Adds a new slot to the
metadata@fcsinfosignature(x = "FCSmetadata")
: prints the
original status, the objectname, filename, and dimensions of the
datasignature(object = "FCSmetadata")
: same as 'print' signature(object = "FCSmetadata")
: summaries
the metadata in a string output
For more information about the different parameters in the
metadata@fcsinfo slot, please look at the documentation for
read.FCS
.
A.J. Rossini, J.Y. Wan, and Zoe Moodie
Trevor Hastie, Robert Tibshirani, and Jerome Friedman. The Elements of Statistical Learning: Data Mining, Inference, and Prediction. Springer Series in Statistics : New York, 2001. pp.279-283.
Jerome H. Friedman and Nicholas I. Fisher. Bump Hunting in High-Dimensional Data. Tech Report. October 28, 1998.
J. Paul Robinson, et al. Current Protocols in Cytometry. John Wiley & Sons, Inc : 2001.
Mario Roederer and Richard R. Hardy. Frequency Difference Gating: A Multivariate Method for Identifying Subsets that Differe between Samples. Cytometry, 45:56-64, 2001.
Mario Roederer and Adam Treister and Wayne Moore and Leonore A. Herzenberg. Probability Binning Comparison: A Metric for Quantitating Univariate Distribution Differences. Cytometry, 45:37-46, 2001.
Keith A. Baggerly. Probability Binning and Testing Agreement between Multivariate Immunofluorescence Histograms: Extending the Chi-Squared Test. Cytometry, 45:141-150, 2001.
read.FCS
,
"FCS-class"
,
"print-methods"
,
"show-methods"
,
"summary-methods"
,
"[-methods"
,
"[[-methods"
,
"[<--methods"
,
"[[<--methods"
default<-new("FCSmetadata") some.meta<-new("FCSmetadata", fcsinfo=list("comment"=rep("none", 10)), mode="none", nparam=0, size=0) ## extract/subset the metadata some.meta[["nparam"]] some.meta["paramranges"] ## replace the metadata/subsetassign the metadata ## 3 parameters with ranges some.meta[["nparam"]]<-3 some.meta["paramranges"]<-rep(1,3) ## show show(some.meta) ## print print(some.meta) some.meta ## summary summary(some.meta)