read.cds: Read the CDS of a given organism

In HajkD/seqreadr: Read Biological Sequence File Formats

Description

Read an organism specific Coding Sequence (CDS) file stored in fasta or fastq format. In case the input file includes corrupt sequences (= sequences that do not fulfill the triplet criteria) users can specify the delete.corrupt = TRUE argument to remove corrupt sequences from the input file.

Usage

read.cds(file, format, 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 CDS, e.g. "fasta", "fatsq".
delete.corrupt	a logical value indicating whether corrupt base triplets should be removed from the input file.
...	additional arguments that are used by the readDNAStringSet function.

Details

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

For example, CDS files fulfilling the fasta file format can be downloaded from http://www.ensembl.org/info/data/ftp/index.html.

Alternatively users

Value

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.

Author(s)

Hajk-Georg Drost

Examples

### Example Non-Corrupt File
# reading a cds file stored in fasta format
Ath.cds <- read.cds(system.file('seqs/ortho_thal_cds.fasta', package = 'seqreadr'),
                    format = "fasta")

dplyr::glimpse(Ath.cds)

### Example Corrupt File
# reading a cds file stored in fasta format
Ath.cds <- read.cds(system.file('seqs/ortho_thal_cds_corrupt.fasta', package = 'seqreadr'),
                    format         = "fasta",
                    delete.corrupt = TRUE)
                    
dplyr::glimpse(Ath.cds)                   

HajkD/seqreadr documentation built on May 6, 2019, 10:55 p.m.