read_cds {biomartr}

Import CDS as Biostrings or data.table object

Description

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

Usage

read_cds(
  file,
  format = "fasta",
  obj.type = "Biostrings",
  delete_corrupt = FALSE,
  ...
)

Arguments

file

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

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".

delete_corrupt

a logical value specifying whether potential CDS sequences that cannot be divided by 3 shall be be excluded from the the dataset. Default is delete_corrupt = FALSE.

...

additional arguments that are used by read.fasta.

Details

The read.cds function takes a string specifying the path to the cds file of interest as first argument.

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

CDS stored in fasta files can be downloaded from http://www.ensembl.org/info/data/ftp/index.html.

Value

A data.table storing the gene id in the first column and the corresponding sequence as string in the second column.

Author(s)

Hajk-Georg Drost

See Also

Other cds: getCDSSet(), getCDS()

Other readers: read_genome(), read_gff(), read_proteome(), read_rna()