protti: extract_metal_binders – R documentation

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extract_metal_binders

Extract metal-bind protein information from UniProt

Description

Information of metal binding proteins is extracted from UniProt data retrieved with fetch_uniprot. ChEBI IDs, potential sub-IDs for metal cations, binding site locations in the protein and sub-ID evidence level (based on metal presence as cofactor) are extracted.

Usage

extract_metal_binders(
  data,
  protein_id = id,
  feature_metal_binding = feature_metal_binding,
  chebi_cofactor = chebi_cofactor,
  chebi_catalytic_activity = chebi_catalytic_activity,
  chebi_data = NULL,
  chebi_relation_data = NULL
)

Arguments

`data`	A data frame containing at least the input columns.
`protein_id`	The name of the column containing protein identifiers.
`feature_metal_binding`	The name of the column containing feature metal binding information from UniProt.
`chebi_cofactor`	The name of the column containing ChEBI cofactor information from UniProt.
`chebi_catalytic_activity`	The name of the column containing ChEBI catalytic activity information from UniProt.
`chebi_data`	Optional, a data frame that can be manually obtained with `fetch_chebi()`. If not provided it will be fetched within the function. If the function is run many times it is recommended to provide the data frame to save time.
`chebi_relation_data`	Optional, a data frame that can be manually obtained with `fetch_chebi(relation = TRUE)`. If not provided it will be fetched within the function. If the function is run many times it is recommended to provide the data frame to save time.

Value

A data frame containing information on protein metal binding state. It contains the following types of columns (the naming might vary based on the input):

protein_id: UniProt protein identifier.
source: The source of the information, can be either feature_metal_binding, chebi_cofactor or chebi_catalytic_activity.
ids: ChEBI ID assigned to protein and binding site based on metal_type column name. These are general IDs that have sub-IDs. Thus, they generally describe the type of metal ion bound to the protein.
metal_position: Amino acid position within the protein that is involved in metal binding.
metal_type: Metal name extracted from feature_metal_binding information. This is the name that is used as a search pattern in order to assign a ChEBI ID with the split_metal_name helper function within this function.
sub_ids: ChEBI ID that is a sub-ID (incoming) of the ID in the ids column. Thus, they more specifically describe the potential nature of the metal ion.
main_id_name: Official ChEBI name associated with the ID in the ids column.
multi_evidence: If there is overlapping information in feature_metal_binding and chebi_cofactor or chebi_catalytic_activity, only feature_metal_binding is retained and multi_evidence is TRUE.
sub_id_name: Official ChEBI name associated with the ID in the sub_ids column.

Examples

## Not run: 
extract_metal_binders(
  data,
  protein_id = id,
  feature_metal_binding = feature_metal_binding,
  chebi_cofactor = chebi_cofactor,
  chebi_catalytic_activity = chebi_catalytic_activity
)

## 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