proteinInfo-methods {isobar} | R Documentation

## Methods for Function proteinInfo

### 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")

[Package isobar version 1.38.0 Index]