proteinInfo-methods: Methods for Function proteinInfo

In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description

proteinInfo slot in Proteingroup objects contains information about proteins. proteinInfo method allows to get and set it.

getProteinInfoFromUniprot downloads information of contained proteins from Uniprot, getProteinInfoFromBiomart from Biomart.

Usage

  ## S4 method for signature 'ProteinGroup'
proteinInfo(x)

  ## S4 method for signature 'ProteinGroup,character,missing'
proteinInfo(x, protein.g, select="name", collapse=", ",
                                                 simplify = TRUE, do.warn = TRUE)

  ## S4 method for signature 'ProteinGroup,missing,character'
proteinInfo(x, protein.ac, select="name", collapse=", ",
                                                 simplify = TRUE, do.warn = TRUE)


  proteinInfoIsOnSpliceVariants(protein.info)

#  getProteinInfoFromUniprot(x, splice.by = 200, fields = c(accession = "id", name
#                 = "entry%20name", protein_name = "protein%20names",
#                 gene_name = "genes", organism = "organism", length =
#                 "length", sequence = "sequence"))


  getProteinInfoFromTheInternet(x)

  getProteinInfoFromNextProt(x)

  getProteinInfoFromBiomart(x, database = "Uniprot")

  getProteinInfoFromBioDb(x, ..., con = NULL)

  getProteinInfoFromEntrez(x, splice.by = 200)

Arguments

x	ProteinGroup object
protein.g	Protein group identifier. If supplied, only information for these proteins is returned.
protein.ac	Protein ACs. If supplied, only information for these proteins is returned.
select	indicating columns to select. See Details.
collapse	passed to paste to concatenate information of multiple protein in one protein group.
simplify	If true, a vector or matrix is returned, with the pasted protein information. If false, a list is returned.
do.warn	If true, report diagnostic warning messages.
splice.by	Chunk size for query of Uniprot database.
database	database from which the ACs stem from. Only Uniprot is supported for now.
con	database connection
fields	mapping of CSV field names to proteinInfo field names
...	arguments to build database connection.
protein.info	protein info data.frame

Details

proteinInfo contains columns accession, name, gene_name, protein_name, and possibly length and sequence. accession is mapped with the entry AC is mapped to the entry AC in the database. getProteinInfoFromUniprot is the preferred methods to get the information. getProteinInfoFromBioDb is an example how to implement the query on a local database. Depending on the database, protein information might be available on protein ACs or also on the specific splice variants. This can be queried with the proteinInfoIsOnSpliceVariants function.

See Also

protein.g

Examples

data(ibspiked_set1)
pg <- proteinGroup(ibspiked_set1)

## Not run: 
  proteinInfo(pg) <- getProteinInfoFromUniprot(pg)
  proteinInfo(pg) <- getProteinInfoFromBiomart(pg)

## End(Not run)

proteinInfo(pg,protein.g="P13635")
protein.g(pg,"CERU")

isobar documentation built on Nov. 8, 2020, 7:48 p.m.