mapSummarizedExperimentOntoGraph: Map experimental data onto a graph

In ccb-hms/BioPlex: R-side access to BioPlex protein-protein interaction data

Map experimental data onto a graph

Description

Functionality for mapping experimental data stored in a SummarizedExperiment onto a graph object.

Usage

mapSummarizedExperimentOntoGraph(
  gr,
  se,
  col.names = NULL,
  rowdata.cols = NULL,
  prefix = ""
)

Arguments

gr	an object of class graph.
se	an object of class SummarizedExperiment.
col.names	character. Column names of se for which assay data should be mapped onto the nodes of gr. Defaults to NULL which will then use all column names of se.
rowdata.cols	character. Column names of rowData(se) which should be mapped onto the nodes of gr. Defaults to NULL which will then use all column names of rowData(se).
prefix	character. Informative prefix that should be pasted together with the selected col.names and rowdata.cols to allow easy identification of columns of interest when mapping from multiple experimental datasets.

Value

An object of class graph.

Examples

# (1) Obtain the latest version of the 293T PPI network ...
bp.293t <- getBioPlex(cell.line = "293T", version = "3.0")

# (2) ... and turn into a graph
bp.gr <- bioplex2graph(bp.293t)

# (3) Obtain the BioPlex3 proteome data ...
se <- getBioplexProteome()

# (4) ... and map onto the graph
bp.gr <- mapSummarizedExperimentOntoGraph(bp.gr, se)

ccb-hms/BioPlex documentation built on Aug. 5, 2023, 9:15 p.m.