investigates a flowCore::tranformList object to get the type and parameters of the transformation applying to a specific channel
Value
If the transformation exists for the specified channel, and is either recognized as a logicle transfo or a linear transfo, a list with two slots:
$type a character containing the transfo type ('logicle' or 'linear')
$params_list a list of named numeric, according to transfo type
Otherwise, NULL is returned.
Examples
data(OMIP021Samples)
# set-up a hybrid transformation list :
# - two channels are logicle-ly transformed with automatic param estimates
# - one channel has explicit logicle transfo with default parameters
# - one channel has linear transformation
# - other channels have no transformation
translist <- flowCore::estimateLogicle(
OMIP021Samples[[1]],
c("450/50Violet-A", "525/50Violet-A")
)
translist <- c(
translist,
flowCore::transformList(
"FSC-A",
flowCore::linearTransform(
a = 0.1,
b = 0
)
),
flowCore::transformList(
"540/30Violet-A",
flowCore::logicleTransform()
)
)
ret1 <- getTransfoParams(translist, channel = "FSC-A")
ret1$type # "linear"
#> [1] "linear"
ret1$paramsList # a = 0.1, b = 0.
#> $a
#> [1] 0.1
#>
#> $b
#> [1] 0
#>
ret2 <- getTransfoParams(translist, channel = "525/50Violet-A")
ret2$type # "logicle"
#> [1] "logicle"
ret2$paramsList # a = 0., w = 0.2834, m = 4.5, t = 262143
#> $a
#> [1] 0
#>
#> $w
#> [1] 0.2628157
#>
#> $m
#> [1] 4.5
#>
#> $t
#> [1] 262143
#>
ret3 <- getTransfoParams(translist, channel = "540/30Violet-A")
ret3$type # "logicle
#> [1] "logicle"
ret3$paramsList # a = 0., w = 0.5, m = 4.5, t = 262144
#> $a
#> [1] 0
#>
#> $w
#> [1] 0.5
#>
#> $m
#> [1] 4.5
#>
#> $t
#> [1] 262144
#>