Import Proteome as Biostrings or data.table object — read_proteome • biomartr
Description: This function reads an organism specific proteome stored in a defined file format.

# Import Proteome as Biostrings or data.table object

Source: `R/read_proteome.R`
`read_proteome.Rd`

This function reads an organism specific proteome stored in a defined file format.

    read_proteome(file, format = "fasta", obj.type = "Biostrings", ...)

## Arguments

file

  a character string specifying the path to the file storing the proteome.

format

  a character string specifying the file format used to store the genome, e.g. `format = "fasta"` (default) or `format = "gbk"`.

obj.type

  a character string specifying the object stype in which the genomic sequence shall be represented. Either as `obj.type = "Biostrings"` (default) or as `obj.type = "data.table"`.

...

  additional arguments that are used by `read.fasta`.

## Value

Either a `Biostrings` or `data.table` object.

## Details

This function takes a string specifying the path to the proteome file of interest as first argument.

It is possible to read in different proteome file standards such as fasta or genebank.

## See also

Other readers: `read_cds()`, `read_genome()`, `read_gff()`, `read_rna()`

Other proteome: `getProteomeSet()`, `getProteome()`

## Author

Hajk-Georg Drost