joinAssays: Join assays in a QFeatures object

In lgatto/Features: Quantitative features for mass spectrometry data

Join assays in a QFeatures object

Description

This function applies a full-join type of operation on 2 or more assays in a QFeatures instance.

Usage

joinAssays(x, i, name = "joinedAssay")

Arguments

x	An instance of class QFeatures.
i	The indices or names of al least two assays to be joined.
name	A character(1) naming the new assay. Default is joinedAssay. Note that the function will fail if there's already an assay with name.

Details

The rows to be joined are chosen based on the rownames of the respective assays. It is the user's responsability to make sure these are meaningful, such as for example refering to unique peptide sequences or proteins.

The join operation acts along the rows and expects the samples (columns) of the assays to be disjoint, i.e. the assays mustn't share any samples. Rows that aren't present in an assay are set to NA when merged.

The rowData slots are also joined. However, only columns that are shared and that have the same values for matching columns/rows are retained. For example of a feature variable A in sample S1 contains value a1 and variable A in sample S2 in a different assay contains a2, then the feature variable A is dropped in the merged assay.

The joined assay is linked to its parent assays through an AssayLink object. The link between the child assay and the parent assays is based on the assay row names, just like the procedure for joining the parent assays.

Value

A QFeatures object with an additional assay.

Author(s)

Laurent Gatto

Examples

## -----------------------------------------------
## An example QFeatures with 3 assays to be joined
## -----------------------------------------------
data(feat2)
feat2

feat2 <- joinAssays(feat2, 1:3)

## Individual assays to be joined, each with 4 samples and a
## variable number of rows.
assay(feat2[[1]])
assay(feat2[[2]])
assay(feat2[[3]])

## The joined assay contains 14 rows (corresponding to the union
## of those in the initial assays) and 12 samples
assay(feat2[["joinedAssay"]])

## The individual rowData to be joined.
rowData(feat2[[1]])
rowData(feat2[[2]])
rowData(feat2[[3]])

## Only the 'Prot' variable is retained because it is shared among
## all assays and the values and coherent across samples (the
## value of 'Prot' for row 'j' is always 'Pj'). The variable 'y' is
## missing in 'assay1' and while variable 'x' is present is all
## assays, the values for the shared rows are different.
rowData(feat2[["joinedAssay"]])

lgatto/Features documentation built on Dec. 25, 2024, 5:50 a.m.