protti: network_analysis – R documentation

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network_analysis

Analyse protein interaction network for significant hits

Description

The STRING database provides a resource for known and predicted protein-protein interactions. The type of interactions include direct (physical) and indirect (functional) interactions. Through the R package STRINGdb this resource if provided to R users. This function provides a convenient wrapper for STRINGdb functions that allow an easy use within the protti pipeline.

Usage

network_analysis(
  data,
  protein_id,
  string_id,
  organism_id,
  score_threshold = 900,
  binds_treatment = NULL,
  halo_color = NULL,
  plot = TRUE
)

Arguments

`data`	A data frame that contains significantly changing proteins (STRINGdb is only able to plot 400 proteins at a time so do not provide more for network plots). Information about treatment binding can be provided and will be displayed as colorful halos around the proteins in the network.
`protein_id`	The name of the column containing the protein accession numbers.
`string_id`	The name of the column containing STRING database identifiers. These can be obtained from UniProt.
`organism_id`	Numeric organism ID (NCBI taxon-ID). This can be obtained from here. H. sapiens: 9606, S. cerevisiae: 4932, E. coli: 511145.
`score_threshold`	The interaction score based on STRING has to be between 0 and 1000. A score closer to 1000 is related to a higher confidence for the interaction. The default value is 900.
`binds_treatment`	The name of the column containing a logical indicating if the corresponding protein binds to the treatment. This information can be obtained from different databases, e.g UniProt.
`halo_color`	Optional, A character vector with a color hex-code. This is the color of the halo of proteins that bind the treatment.
`plot`	A logical indicating whether the result should be plotted or returned as a table.

Value

A network plot displaying interactions of the provided proteins. If binds_treatment was provided halos around the proteins show which proteins interact with the treatment. If plot = FALSE a table with interaction information is returned.

Examples

## Not run: 
network_analysis(
  data,
  protein_id = pg_protein_accessions,
  string_id = database_string,
  organism_id = 511145,
  binds_treatment = is_known,
  plot = TRUE
)

## End(Not run)

protti

Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

v0.1.1

MIT + file LICENSE

Authors

Jan-Philipp Quast [aut, cre], Dina Schuster [aut], ETH Zurich [cph, fnd]

Initial release