read.proteome: Read the proteome of a given organism
In HajkD/seqreadr: Read Biological Sequence File Formats

Description Usage Arguments Details Value Author(s) Examples

Read an organism specific proteome stored in a fasta/fastq file format.

1	read.proteome(file, format, ...)

`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 proteome, e.g. `format = "fasta"` or `format = "fastq"`.
`...`	additional arguments that are used by the `readAAStringSet` function.

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 fastq.

Proteomes stored in fasta format can be downloaded from http://www.ebi.ac.uk/reference_proteomes.

A data.frame storing the gene id in the first column, the corresponding sequence as string in the second column, and the sequence length in the third column.

Hajk-Georg Drost

# reading a proteome stored in a fasta file
Ath.proteome <- read.proteome(system.file('seqs/ortho_thal_aa.fasta', package = 'seqreadr'),
                               format = "fasta")

dplyr::glimpse(Ath.proteome)