Subset flowstate[['data']] — subset.flowstate • flowstate

Subset flowstate[['data']] and return a new flowstate object.

Usage

# S3 method for class 'flowstate'
subset(x, ...)

Arguments

x: A flowstate object as returned from read.flowstate.
...: subset argument as defined by data.table's subset; logical expression indicating elements or rows to keep.

Value

A flowstate object whose [['data']] element (a data.table) has been subset to contain the rows as defined through the subset argument. Other elements of x are copied.

Examples

fcs.file.paths <- system.file("extdata", package = "flowstate") |>
list.files(full.names = TRUE, pattern = "BLOCK.*.fcs")

#read all .fcs files as flowstate objects; concatenate into a single object
fs <- read.flowstate(
  fcs.file.paths,
  colnames.type="S",
  concatenate = TRUE
)
#> COVAIL_002_CYTOKINE_BLOCK1_1.fcs --> flowstate
#> COVAIL_002_CYTOKINE_BLOCK1_2.fcs --> flowstate
#> COVAIL_002_CYTOKINE_BLOCK1_3.fcs --> flowstate
#> Concatenating 'flowstate.ojects'...

#transform
flowstate.transform(fs,'CD3')
#> flowstate.object --> transforming...

#plot;visualize valley
fs$data[,plot(density(CD3))]
#> NULL
abline(v = 1.1)#not data-driven; just for example


#subset
fs.cd3_positive <- subset(fs,CD3 > 1.1)

#totals
fs$data[,.N]
#> [1] 6000
fs.cd3_positive$data[,.N]
#> [1] 4032