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

read.cds(file, format, delete_corrupt_cds = TRUE, ...)

## Arguments

file a character string specifying the path to the file storing the CDS. a character string specifying the file format used to store the CDS, e.g. "fasta", "fatsq". a logical value indicating whether sequences with corrupt base triplets should be removed from the input file. This is the case when the length of coding sequences cannot be divided by 3 and thus the coding sequence contains at least one corrupt base triplet. additional arguments that are used by the readDNAStringSet function.

## Value

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

## 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 fastq.

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