getIndexSort: Extract Index Sorted Data from an FCS File

Description Details Value Methods Author(s) Examples


Retrieve a data frame of index sorted data and sort indices from an FCS file.


The input FCS file should already be compensated. Index sorting permits association of cell-level fluorescence intensities with downstream data collection on the sorted cells. Cells are sorted into a plate with X,Y coordinates, and those coordinates are stored in the FCS file.

This function will extract the data frame of flow data and the X,Y coordinates for the cell-level data, which can be written to a text file, or concatenated with sample-level information and analyzed in R. The coordinates are names 'XLoc','YLoc', and a 'name' column is also prepended with the FCS file name.


Matrix of fluorescence intensities and sort indices for plate location. When no index sorting data is available, invisibly returns 0. Test for 0 to check success.


getIndexSort(x = "flowFrame")

Return a matrix of fluorescence intensities and indices into the sorting plate for each cell.


G. Finak


 samp <- read.FCS(system.file("extdata","0877408774.B08", package="flowCore"))
 # This will return a message that no index sorting data is available

flowCore documentation built on Nov. 8, 2020, 5:19 p.m.