"fixvars-methods" {rflowcyt} | R Documentation

## Checks and fixes 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 and will be updated with the descriptives from the data. The following is a description of the checks and fixes:

1. Dimension check and fix
  We always check the dimensions (ie, if the data dimensions match with size ($TOT) and nparam ($PAR) that are specified in the metadata. If they are not in check, then the metadata parameters are changed to reflect the values of the data dimensions.
2. Parameter Name check and fix
  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. Depending on the number of discrepancies (ie, the one with the least number of discrepanices; by default the longnames if there is a tie), either the longnames or the shortnames of the metadata are replaced with the column names of the data.
3. Column Variable Range Check
  We check the paramranges ($PnR) specified in the metadata with the column parameter ranges of the data; if there are any discrepancies, then the paramranges are replaced with the maximum values of the data columns.

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"
  A `FCS`object will be returned with any fixes to the metadata.
x = "FCS", x.name="", MY.DEBUG=TRUE, range.max=NULL
  Other options in the signature include:

  (1) x.name : character string of the true object name; default is "" (ie, the objectname in the metadata will be regarded as the true object name )

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

  (3) 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 1.16.0 Index]