"checkvars-methods" {rflowcyt} | R Documentation

## Checks the ranges, dimensions, and names of the metadata based on the current data of an FCS R-object.

### Description

Any discrepancy between the metadata and the data of the FCS object is considered as a failure to pass the check. The following is a description of the checks:

1. Dimension check
  We always check the dimensions (ie, if the data dimensions match with size ("$TOT") and nparam ("$PAR") that are specified in the metadata).
2. Parameter Name check
  We check the names of the metadata with the names of the data column parameters. Either only the longnames ("$PnS") or the shortnames ("$PnN") of the metadata are checked against the names of the data. Please take note that both ("$PnS") and ("$PnN") ARE NOT BOTH checked.
3. Column Variable Range Check
  We check the paramranges ("$PnR") specified in the metadata with the column parameter ranges of the data; if the paramranges do not exist in the metadata, then it is noted in the debugging statements.

Please note that if the metadata@original is FALSE, then the metadata slotNames have a "RFACSadd$>>$" suffix and are located in metadata@fcsinfo in order to store the current data descriptives. The original data descriptives can be retrieved/checked when metadata@original is set to TRUE; otherwise the current metadata information about the data is retrieved/checked even when the "RFACSadd$>>$" suffix is not noted in the character index.

(ie) If metadata@original is FALSE, then metadata[["size"]] will return metadata[["RFACSadd$>>$$TOT"]], the current row length of the data, while metadata@size will return the number of rows for the original data.

Note that metadata@original is changed only when a parameter column is added to the data using `addParameter-methods`, when rows of the data are extracted using `extractGatedData` or if the user decides to change the value metadata@original. Using `"["-methods` and `"[<-"-methods` on a "FCS" object will not change the value of metadata@original.

### Methods

x = "FCS"
  boolean value is returned; TRUE if the check passes and FALSE if it does not pass the check.
x = "FCS", MY.DEBUG=TRUE, range.max=NULL
  Other options in the signature include:

  (1) MY.DEBUG : boolean value; if TRUE, then the output statements are printed, otherwise if FALSE, then the statements are surpressed; default is TRUE.

  (2) range.max : numeric value describing the true maximum of the data that the checks on the ranges will be compared; default is NULL (ie, the maximum of each column variable in the data is the truth)

[Package rflowcyt version 1.12.0 Index]