"FCSmetadata-class" {rflowcyt} | R Documentation

## Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object

### Description

Information from the HEADER and TEXT of a raw binary FCS file about the data and other parameters are stored in the metadata.

### Objects from the Class

Objects can be created by calls of the form `new("FCSmetadata", ...)`.

### Slots

`mode`:
  Object of class `"character"` the "$MODE" mode of the raw binary FCS file
`size`:
  Object of class `"numeric"` the "$TOT" row dimension of the data; describing the number of observations or cells
`nparam`:
  Object of class `"numeric"` the "$PAR" column dimension of the data; describing the number of parameters
`shortnames`:
  Object of class `"vector"` the "$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 data
`longnames`:
  Object of class `"vector"` the "$PnS" long names used for the column variables of the data
`paramranges`:
  Object of class `"vector"` the "$PnR" maximum value corresponding to the column variables
`filename`:
  Object of class `"character"` path and/or name of the original raw binary FCS object
`objectname`:
  Object of class `"character"` the name of the original, `FCS-class` object
`original`:
  Object of class `"logical"` the original status of the current object
`fcsinfo`:
  Object of class `"list"` the other parameters and values in the HEADER and TEXT of the raw binary FCS file

### Methods

"["
  `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@fcsinfo
"print-methods"
  `signature(x = "FCSmetadata")`: prints the original status, the objectname, filename, and dimensions of the data
"show-methods"
  `signature(object = "FCSmetadata")`: same as 'print'
"summary-methods"
  `signature(object = "FCSmetadata")`: summaries the metadata in a string output

### Note

For more information about the different parameters in the metadata@fcsinfo slot, please look at the documentation for `read.FCS`.

### Author(s)

A.J. Rossini, J.Y. Wan, and Zoe Moodie

### References

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.

### See Also

`read.FCS`, `"FCS-class"`, `"print-methods"`, `"show-methods"`, `"summary-methods"`, `"[-methods"`, `"[[-methods"`, `"[<--methods"`, `"[[<--methods"`

### Examples

    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)

[Package rflowcyt version 1.12.0 Index]