pmartR (version 2.4.6)

edata_transform: Apply a Transformation to the Data

Description

This function applies a transformation to the e_data element of omicsData

Usage

edata_transform(omicsData, data_scale)

Value

data object of the same class as omicsData

Arguments

omicsData

an object of the class 'pepData', 'proData', 'metabData', 'lipidData', or 'nmrData', created by as.pepData, as.proData, as.metabData, as.lipidData, or as.nmrData, respectively.

data_scale

a character string indicating the type of transformation to be applied to the data. Valid values for 'pepData', 'proData', 'metabData', 'lipidData', or 'nmrData': 'log2', 'log', 'log10', or 'abundance'. A value of 'abundance' indicates the data has previously undergone one of the log transformations and should be transformed back to raw values with no transformation applied.

Valid values for 'seqData': 'upper', 'median', 'lcpm'. For 'seqData', 'lcpm' transforms by log2 counts per million, 'upper' transforms by the upper quartile of non-zero counts, and 'median' transforms by the median of non-zero counts.

Author

Kelly Stratton, Natalie Heller

Details

For all but seqData, this function is intended to be used before analysis of the data begins, and data are typically analyzed on a log scale. This function is not applicable to seqData objects, as any transformations needed e.g. to allow more meaningful visualization of seqData objects are performed within the pertinent functions.

Examples

if (FALSE) { # requireNamespace("pmartRdata", quietly = TRUE)
library(pmartRdata)
mymetab <- edata_transform(omicsData = metab_object, data_scale = "log2")
attr(mymetab, "data_info")$data_scale
}