dot-transformOnDiskMSnExp: Transformation of OnDiskMSnExp

In LiesaSalzer/mobilityTransformationR: Effective mobility scale transformation of CE-MS(/MS) data

Transformation of OnDiskMSnExp

Description

Transformation of OnDiskMSnExp

Usage

.transformOnDiskMSnExp(x, marker, tR = tR, U = U, L = L)

Arguments

x	OnDiskMSnExp-object that stores the migration times in seconds.
marker	data.frame containing minimum two columns, where one holds the determined migration time in minutes (here referred to as "rtime") of the EOF marker in the same run in which the migration time is going to be transformed and the other column the respective mobility ("mobility") of the EOF markers. Each row hold the values for one EOF marker. If OnDiskMSnExp is used in x, a third column "fileIdx" is required, that stores the file Index. One or two entries are required per file for the transformation and depending on the number of entries the transformation will be performed either on one or both markers.
tR	numeric a single value that defines the time (in minutes) of the electrical field ramp. The default is 0.
U	numeric a single value that defines the voltage (in kV) applied. Note that for reversed polarity CE mode a negative value is needed.
L	numeric a single value that defines the total length (in mm) of the capillary that was used for CE(-MS) analysis.

Value

OnDiskMSnExp-Object that stores the effective mobility in mm^2 / (kV * min).

Examples

fl <- system.file("CE-MS/CEMS_10ppm.mzML",
    package = "msdata"
)
raw_data <- MSnbase::readMSData(
    files = fl,
    mode = "onDisk"
)

marker <- data.frame(
    markerID = c("marker1", "marker2"),
    rtime = c(20, 80),
    mobility = c(0, 2000),
    fileIdx = c(1, 1)
)

MobilityTransformR:::.transformOnDiskMSnExp(
    x = raw_data, marker = marker,
    tR = 3, U = 30, L = 90
)

LiesaSalzer/mobilityTransformationR documentation built on April 3, 2022, 5:58 p.m.