Package 'BioPlex'

Title: R-side access to BioPlex protein-protein interaction data
Description: The BioPlex package implements access to the BioPlex protein-protein interaction networks and related resources from within R. Besides protein-protein interaction networks for HEK293 and HCT116 cells, this includes access to CORUM protein complex data, and transcriptome and proteome data for the two cell lines. Functionality focuses on importing the various data resources and storing them in dedicated Bioconductor data structures, as a foundation for integrative downstream analysis of the data.
Authors: Ludwig Geistlinger [aut, cre], Robert Gentleman [aut]
Maintainer: Ludwig Geistlinger <[email protected]>
License: Artistic-2.0
Version: 1.18.0
Built: 2026-10-10 11:18:33 UTC
Source: https://github.com/bioc/BioPlex

Help Index

Annotate PFAM domains to BioPlex PPI graph

Description

This function adds PFAM domain annotations to the node metadata of the BioPlex PPI graph.

Usage

annotatePFAM(bp.gr, orgdb)

Arguments

bp.gr

an object of class graph storing the BioPlex PPIs. Typically obtained via bioplex2graph.
orgdb

an orgdb object storing annotation data for human.

Value

An object of class graphNEL containing PFAM domain annotations in the nodeData.

References

BioPlex: https://bioplex.hms.harvard.edu/interactions.php

PFAM: http://pfam.xfam.org

See Also

nodeData

Examples

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

# (2) Turn the data into a graph 
bp.gr <- bioplex2graph(bp.293t)

# (3) Obtain orgdb package from AnnotationHub
ah <- AnnotationHub::AnnotationHub()
orgdb <- AnnotationHub::query(ah, c("orgDb", "Homo sapiens"))
orgdb <- orgdb[[1]]

# (4) Annotate PFAM domains
bp.gr <- annotatePFAM(bp.gr, orgdb)

Representation of BioPlex PPIs in a graph data structure

Description

Representation of BioPlex PPIs in a graphNEL object from the graph package.

Usage

bioplex2graph(bioplex.df)

Arguments

bioplex.df

a data.frame storing the Bioplex PPIs in a flat from-to format. Typically obtained via getBioPlex.

Value

An object of class graphNEL.

References

BioPlex: https://bioplex.hms.harvard.edu/interactions.php

See Also

getBioPlex, ftM2graphNEL

Examples

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

# (2) Turn the data into a graph 
bp.gr <- bioplex2graph(bp.293t)

Convenient access to the CCLE proteome data

Description

Functionality for storing the protein expression data from the Cancer Cell Line Encyclopedia (CCLE) in a SummarizedExperiment.

Usage

ccleProteome2SummarizedExperiment(df, cell.line = "HCT116")

Arguments

df

a data.frame storing the CCLE protein expression data with one measurement in each row. Typically obtained from ExperimentHub. See examples.
cell.line

character. One or more cell line IDs such as "HCT116" (human colon cancer cell line 116). Use NULL to not subset by cell line. Defaults to "HCT116", which will then subset the df to measurements for HCT116 only.

Value

A SummarizedExperiment storing protein expression data for the specified cell line(s).

References

CCLE proteomics: https://gygi.hms.harvard.edu/publications/ccle.html

Examples

# Connect to ExperimentHub
  eh <- ExperimentHub::ExperimentHub()

  # Obtain CCLE proteome data frame
  AnnotationHub::query(eh, c("gygi", "depmap"))
  ccle.prot <- eh[["EH3459"]]
  ccle.prot <- as.data.frame(ccle.prot)

  # Turn into a SummarizedExperiment
  se <- ccleProteome2SummarizedExperiment(ccle.prot)

Represent CORUM protein complex data as a list of graph instances

Description

Functionality for storing CORUM protein complex data in a list of graph instances.

Usage

corum2graphlist(corum.df, subunit.id.type = c("UNIPROT", "ENTREZID"))

Arguments

corum.df

A data.frame storing the CORUM protein complex data. Typically obtained via getCorum.
subunit.id.type

character. Supported options include "UNIPROT" (default) and "ENTREZID".

Value

A list with an entry for each complex. Each entry is an object of class graphNEL connecting all subunit IDs with each other by undirected edges.

References

CORUM: http://mips.helmholtz-muenchen.de/corum/#download

Examples

# (1) Obtain the core set of CORUM complexes ...
 core <- getCorum(set = "core")
 
 # (2) ... turn into a list of graphs
 core.glist <- corum2graphlist(core)

Represent CORUM protein complex data as a simple list

Description

Functionality for storing CORUM protein complex data in a list.

Usage

corum2list(corum.df, subunit.id.type = c("UNIPROT", "ENTREZID"))

Arguments

corum.df

A data.frame storing the CORUM protein complex data. Typically obtained via getCorum.
subunit.id.type

character. Supported options include "UNIPROT" (default) and "ENTREZID".

Value

A list with an entry for each complex. Each entry is a character vector of subunit IDs.

References

CORUM: http://mips.helmholtz-muenchen.de/corum/#download

Examples

# (1) Obtain the core set of CORUM complexes ...
 core <- getCorum(set = "core")
 
 # (2) ... turn into a list
 core.list <- corum2list(core)

Obtain BioPlex protein-protein interaction data

Description

Functionality for retrieving the BioPlex protein-protein interaction data. Available networks include:

  • BioPlex 293T cells (versions 1.0, 2.0, and 3.0),

  • BioPlex HCT116 cells (version 1.0).

See references.

Usage

getBioPlex(
  cell.line = c("293T", "HCT116"),
  version = c("3.0", "1.0", "2.0"),
  remap.uniprot.ids = FALSE,
  cache = TRUE
)

Arguments

cell.line

character. Valid options include:

  • "293T": derivative of human embryonic kidney 293 cell line,

  • "HCT116": human colon cancer cell line 116.

Defaults to "293T".
version

character. Valid options include "1.0", "2.0", and "3.0" for 293T cells. For HCT116 cells, only "1.0" is available. Defaults to "3.0".
remap.uniprot.ids

logical. Should the protein-to-gene mappings from BioPlex (i.e. UNIPROT-to-SYMBOL and UNIPROT-to-ENTREZID) be updated using Bioc annotation functionality? Defaults to FALSE which will then keep the mappings provided by BioPlex.
cache

logical. Should a locally cached version used if available? Defaults to TRUE.

Value

A data.frame.

References

BioPlex: https://bioplex.hms.harvard.edu/interactions.php

Examples

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

# (2) Obtain the latest version of the HCT116 PPI network
bp.hct116 <- getBioPlex(cell.line = "HCT116", version = "1.0")

Obtain BioPlex3 proteome data

Description

Functionality for retrieving the BioPlex3 protein expression data comparing expression in the HCT116 and the 293T cell lines.

Usage

getBioplexProteome(cache = TRUE)

Arguments

cache

logical. Should a locally cached version used if available? Defaults to TRUE.

Value

A SummarizedExperiment storing protein expression data for the both cell line(s) with 5 replicates each.

References

BioPlex: https://bioplex.hms.harvard.edu

Examples

se <- getBioplexProteome()

Obtain CORUM protein complex data

Description

Functionality for retrieving the CORUM protein complex data. Available complex collections include:

  • complete set of complexes,

  • core set of complexes,

  • complexes with splice variants.

See references.

Usage

getCorum(
  set = c("all", "core", "splice"),
  organism = "Human",
  remap.uniprot.ids = FALSE,
  cache = TRUE,
  mode = c("ehub", "web")
)

Arguments

set

character. Valid options include:

  • "all": complete set of complexes,

  • "core": core set of complexes,

  • "splice": complexes with splice variants.

Defaults to "all".
organism

character. Use NULL to not subset by organism. Defaults to "Human" which restricts the data to human protein complexes only.
remap.uniprot.ids

logical. Should the protein-to-gene mappings from CORUM (i.e. UNIPROT-to-SYMBOL and UNIPROT-to-ENTREZID) be updated using Bioc annotation functionality? Currently only supported in combination with organism = "Human". Defaults to FALSE which will then keep the mappings provided by CORUM.
cache

logical. Should a locally cached version used if available? Defaults to TRUE.
mode

character. Should CORUM complexes be obtained from ExperimentHub or via a web download from the CORUM homepage? Defaults to "ehub", which will obtain the chosen complex set from ExperimentHub.

Value

A data.frame.

References

CORUM: http://mips.helmholtz-muenchen.de/corum/#download

Examples

# Obtain the core set of CORUM complexes
core <- getCorum(set = "core")

Convenient access to 293T transcriptome data from GEO

Description

Functionality for storing the 293T RNA-seq data from GSE122425 in a SummarizedExperiment. The dataset includes three wild type samples and three NSUN2 knockout samples.

Usage

getGSE122425(cache = TRUE)

Arguments

cache

logical. Should a locally cached version used if available? Defaults to TRUE.

Value

A SummarizedExperiment storing RNA-seq data for the 293T cell line.

References

GSE122425: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122425

Examples

# Obtain the data as a SummarizedExperiment
  se <- getGSE122425()

Identify CORUM complexes that have a subunit of interest

Description

Screens a list of graph instances storing CORUM protein complex data for a subunit of choice.

Usage

hasSubunit(glist, subunit, id.type = "SYMBOL")

Arguments

glist

A list of graphs storing CORUM complexes. Typically obtained via corum2graphlist.
subunit

character. A gene ID corresponding to the subunit of interest.
id.type

character. Gene ID type of the given subunit. Defaults to "SYMBOL".

Value

A logical vector indicating which graphs have a node with the given subunit.

Examples

# (1) Obtain the core set of CORUM complexes ...
core <- getCorum(set = "core")

# (2) ... turn into a list of graphs ...
core.glist <- corum2graphlist(core)

# (3) .. check for a particular subunit of interest
has.cdk2 <- hasSubunit(core.glist, subunit = "CDK2")

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)