normalizeSCP {scp}R Documentation

Normalize single-cell proteomics (SCP) data

Description

This function normalises an assay in a QFeatures according to the supplied method (see Details). The normalized data is added as a new assay

Usage

normalizeSCP(object, i, name = "normAssay", method, ...)

Arguments

object

An object of class QFeatures.

i

A numeric vector or a character vector giving the index or the name, respectively, of the assay(s) to be processed.

name

A character(1) naming the new assay name. Defaults is are normAssay.

method

character(1) defining the normalisation method to apply. See Details.'

...

Additional parameters passed to MsCoreUtils::normalizeMethods().

Details

The method parameter in normalize can be one of "sum", "max", "center.mean", "center.median", "div.mean", "div.median", "diff.meda", "quantiles", "quantiles.robust" or "vsn". The MsCoreUtils::normalizeMethods() function returns a vector of available normalisation methods.

For further details and examples about normalisation, see MsCoreUtils::normalize_matrix().

Value

A QFeatures object with an additional assay containing the normalized data.

See Also

QFeatures::normalize for more details about normalize


[Package scp version 1.3.3 Index]