Description Usage Arguments Details Value Author(s) Examples
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.
1 |
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 |
... |
additional arguments that are used by the |
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
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ### 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)
|
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