| "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)