compute linear transformation of scatter channels found in ff, based on 5% and 95% of referenceChannel, set as target. If there is a transformation defined in transList for referenceChannel, it is applied first, before computing quantiles. Then the computed linear transformations (or each scatter channel) are added into the transfo_list. -A channels are computed, and same linear transformation is then applied to corresponding -W and -H channels (if they exist in ff).

based on a referenceChannel

Usage

computeScatterChannelsLinearScale(
  ff,
  transList = NULL,
  referenceChannel,
  silent = TRUE
)

Arguments

ff

a flowCore::flowFrame

transList

an initial flowCore::transformList

referenceChannel

the reference channel to take target quantile values from. Can be defined as marker or channel name.

silent

if FALSE, will output some information on the computed linear transformations

Value

the transList with added linear scale transformations

Examples

data(OMIP021Samples)

ff <- OMIP021Samples[[1]]
refMarker <- "APCCy7 - CD4"
refChannel <- "780/60Red-A"
transList <- flowCore::estimateLogicle(ff,
                                       channels = refChannel)
retTransList <-
    computeScatterChannelsLinearScale(ff,
                                      transList = transList,
                                      referenceChannel = refMarker,
                                      silent = TRUE
    )