getIndexSort: Extract Index Sorted Data from an FCS File
Description
Retrieve a data frame of index sorted data and sort indices from an FCS file.
Arguments
Value
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.
Methods
x = "flowFrame"
Return a matrix of
fluorescence intensities and indices into the sorting plate for each cell.
Details
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.
samp <- read.FCS(system.file("extdata","0877408774.B08", package="flowCore"))
# This will return a message that no index sorting data is available getIndexSort(samp)