Description Usage Arguments Value Examples
RemoveMargins
will remove margin events from the
flowframe based on the internal description of the fcs file.
1 2 | RemoveMargins(ff, channels,
channel_specifications=NULL, output="frame")
|
ff |
A flowframe that contains flow cytometry data. |
channels |
The channel indices or channel names that have to be checked for margin events |
channel_specifications |
A list of lists with parameter specifications
for certain channels. This parameter should only be used if the values in
the internal parameters description is too strict or wrong for a number or
all channels. This should be one list per channel with first a minRange and
then a maxRange value. This list should have the channel name found back in
|
output |
If set to "full", a list with the filtered flowframe and the indices of the margin event is returned. If set to "frame", only the filtered flowframe is returned. The default is "frame". |
This function returns either a filtered flowframe when the
output
parameter is set to "frame" or a list containing the filtered
flowframe and a TRUE/FALSE list indicating the margin events. An extra column
named "Original_ID" is added to the flowframe where the cells are given their
original cell id.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | # Read in raw data
fileName <- system.file("extdata", "111.fcs", package="PeacoQC")
ff <- flowCore::read.FCS(fileName)
# Define channels where the margin events should be removed
channels <- c(1, 3, 5:14, 18, 21)
# Remove margins
ff_cleaned <- RemoveMargins(ff, channels)
# If an internal value is wrong for a channels (e.g. FSC-A)
channel_specifications <- list("FSC-A"=c(-111, 262144))
ff_cleaned <- RemoveMargins(
ff,
channels,
channel_specifications=channel_specifications)
|
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