| Type: | Package |
| Title: | Common Computational Operations Working with RefSeq Entries (GenBank) |
| Version: | 1.1.5 |
| Maintainer: | Jose V. Die <jose.die@uco.es> |
| Description: | Fetches NCBI data (RefSeq https://www.ncbi.nlm.nih.gov/refseq/ database) and provides an environment to extract information at the level of gene, mRNA or protein accessions. |
| License: | MIT + file LICENSE |
| URL: | https://github.com/jdieramon/refseqR |
| BugReports: | https://github.com/jdieramon/refseqR/issues |
| Encoding: | UTF-8 |
| Imports: | IRanges, rentrez, tibble, Biostrings |
| RoxygenNote: | 7.2.3 |
| Suggests: | knitr, rmarkdown |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2024-10-29 23:45:10 UTC; jdieramon |
| Author: | Jose V. Die  [aut,
cre],
Lluís Revilla Sancho
[ctb] |
| Repository: | CRAN |
| Date/Publication: | 2024-10-30 00:50:01 UTC |
refseqR: Common computational operations working with RefSeq
Description
refseqR is a framework of common computational operations working with RefSeq entries (GenBank)
Author(s)
Jose V. Die jose.die@uco.es
See Also
Useful links:
Get the amino acid length from a protein accession
Description
refseq_AAlen() Returns the amino acid length from a single protein accession.
Depending on the function, available accessions in refseqR include RefSeq models with the prefixes XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.
Usage
refseq_AAlen(protein)
Arguments
protein |
A character string of the protein id. |
Value
A numeric value representing the aa length of the protein.
Author(s)
Jose V. Die
See Also
refseq_RNA2protein to obtain the protein ids encoded by a set of transcript ids.
Examples
# Get the amino acid lengths from a set of protein accessions
protein = c("XP_004487758", "XP_004488550")
sapply(protein, function(x) refseq_AAlen(x), USE.NAMES = FALSE)
Get the amino acid length from a protein accession
Description
refseq_AA_len_action() Returns the amino acid length from a single protein accession.
Depending on the function, available accessions in refseqR include RefSeq models with the prefixes XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.
Usage
refseq_AAlen_action(protein, retries)
Arguments
protein |
A character string of the protein id. |
retries |
A numeric value to control the number of retry attempts to handle internet errors. |
Value
A numeric value representing the aa length of the protein.
Author(s)
Jose V. Die
See Also
refseq_RNA2protein to obtain the protein ids encoded by a set of transcript ids.
Extract the molecular weight from a protein accession
Description
refseq_AAmol_wt() Parses a protein accession output (RefSeq format) and extract the molecular weight
(in Daltons).
Depending on the function, available accessions in refseqR include RefSeq models with the prefixes XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.
Usage
refseq_AAmol_wt(protein)
Arguments
protein |
A character string of the protein id. |
Details
First, get the character vector containing the fetched record. Then, this function parses the fetched record and returns the molecular weight.
Value
A numeric vector representing the molecular weight of the protein.
Author(s)
Jose V. Die
See Also
refseq_RNA2protein to obtain the protein ids encoded by a set of transcript ids.
Examples
# Get the molecular weight from a single protein accession
protein <- "XP_020244413"
refseq_AAmol_wt(protein)
# Get the molecular weight from from a set of protein accessions
protein = c("XP_004487758", "XP_004488550")
sapply(protein, function(x) refseq_AAmol_wt(x), USE.NAMES = TRUE)
Extract the amino acid sequence into a Biostrings object
Description
refseq_AAseq() Parses a single/multiple protein accessions (RefSeq format) and extract
the amino acid sequence(s) into a AAStringSet object.
Depending on the function, available accessions in refseqR include RefSeq models with the prefixes XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.
Usage
refseq_AAseq(accession)
Arguments
accession |
A character string containing a single/multiple accession ids. |
Value
An object of AAStringSet class.
Author(s)
Jose V. Die
Examples
accession = c("XP_004487758", "XP_004488550", "XP_004501961")
my_aa <- refseq_AAseq(accession)
# Now, the `AAStringSet`can be easily used to make a fasta file :
# writeXStringSet(x= my_aa, filepath = "aa_result")
Extract the coding sequences (CDS) coordinates from a transcript accession
Description
refseq_CDScoords() Parses a transcript accession (RefSeq format) and extract the CDS coordinates.
The CDS coordinates refer to the mRNA molecule.
Depending on the function, available accessions in refseqR include RefSeq models with the prefixes XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.
Usage
refseq_CDScoords(transcript)
Arguments
transcript |
A character string of the single/multiple transcript id. |
Value
An IRanges object with the start and end position of the CDS of the
putative mRNAs.
Author(s)
Jose V. Die
See Also
Examples
transcript = c("XM_004487701")
refseq_CDScoords(transcript)
transcript = c("XM_004487701", "XM_004488493")
refseq_CDScoords(transcript)
Extract the CDS nucleotide sequence into a Biostrings object
Description
refseq_CDSseq() Parses a single/multiple transcript accessions (RefSeq format) and extract
the CDS nucleotide sequences into a DNAStringSet object.
Depending on the function, available accessions in refseqR include RefSeq models with the prefixes XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.
Usage
refseq_CDSseq(transcript)
Arguments
transcript |
A character string of the single/multiple transcript id. |
Value
An object of DNAStringSet class.
Author(s)
Jose V. Die
See Also
Examples
transcript <- c("XM_004487701", "XM_004488493", "XM_004501904")
my_cds <- refseq_CDSseq(transcript)
# Now, the `DNAStringSet` can easily used to make a fasta file :
# writeXStringSet(x= my_cds, filepath = "cds_result")
Get the GeneID
Description
refseq_GeneID() Returns the GeneID from a single transcript or protein accession.
Depending on the function, available accessions in refseqR include RefSeq models with the prefixes XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.
Usage
refseq_GeneID (accession, db, retries)
Arguments
accession |
A character string of the transcript or protein accession. |
db |
A character string of the "nuccore" or "protein" database. |
retries |
A numeric value to control the number of retry attempts to handle internet errors. |
Value
A character vector containing the GeneID corresponding to the specified accession as accession.
Author(s)
Jose V. Die
See Also
refseq_protein2RNA to obtain the transcript accessions that encode a set of protein accessions.
refseq_RNA2protein to obtain the protein accessions encoded by a set of transcript accessions.
Examples
## Not run:
# Get the gene symbol from a set of transcript accessions
transcript = c("XM_004487701")
sapply(transcript, function(x) refseq_GeneID (x, db = "nuccore", retries = 4), USE.NAMES = FALSE)
# Get the gene symbol from a set of protein accessions
protein = c("XP_004487758")
sapply(protein, function(x) refseq_GeneID (x, db = "protein", retries = 4), USE.NAMES = FALSE)
## End(Not run)
Get the protein accession from the transcript accession
Description
refseq_RNA2protein() Returns the protein accession from a single transcript accession.
Depending on the function, available accessions in refseqR include RefSeq models with the prefixes XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.
Usage
refseq_RNA2protein(transcript)
Arguments
transcript |
A character string of the protein accession. |
Value
A character vector containing the protein id encoded by the mRNA especified as transcript.
Author(s)
Jose V. Die
See Also
refseq_protein2RNA to obtain the transcript ids that encode a set of proteins ids.
Examples
## Not run:
# Get the protein id from a single transcript accession
transcript <- "XM_004487701"
refseq_RNA2protein(transcript)
# Get the protein ids from a set of transcript accessions
transcript = c("XM_004487701", "XM_004488493")
sapply(transcript, function(x) refseq_RNA2protein(x), USE.NAMES = FALSE)
## End(Not run)
Get the sequence Description
Description
refseq_description() Returns the sequence description from a single transcript, protein, or GeneID accession.
Depending on the function, available accessions in refseqR include RefSeq models with the prefixes transcript_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.
Usage
refseq_description(id)
Arguments
id |
A character string of the transcript, protein, or GeneID accession. |
Value
A character vector containing the sequence description corresponding to the specified sequence as id.
Author(s)
Jose V. Die
See Also
refseq_protein2RNA to obtain the transcript ids that encode a set of protein ids.
refseq_RNA2protein to obtain the protein ids encoded by a set of transcript ids.
Examples
## Not run:
# Get the sequence descriptions from a set of transcript accessions
transcript = c("XM_004487701")
sapply(transcript, function(x) refseq_description(x), USE.NAMES = FALSE)
# Get the sequence descriptions from a set of protein accessions
protein = c("XP_004487758")
sapply(protein, function(x) refseq_description(x), USE.NAMES = FALSE)
#' # Get the sequence descriptions from a set of Gene accessions
locs <- c("LOC101512347", "LOC101506901")
sapply(locs, function(x) refseq_description(x), USE.NAMES = FALSE)
## End(Not run)
Get the mRNA or protein accession
Description
refseq_fromGene() Returns the mRNA or protein accession from a single GeneID.
Usage
refseq_fromGene(GeneID, sequence)
Arguments
GeneID |
A character string of the GeneID. |
sequence |
A character string of the mRNA or protein accession to fetch data from mRNA or protein databases, respectively. |
Value
A character vector containing the mRNA or protein accession corresponding to the especified GeneID.
Author(s)
Jose V. Die
See Also
refseq_protein2RNA to obtain the transcript accessions that encode a set of protein accessions.
refseq_RNA2protein to obtain the protein accessions encoded by a set of transcript accessions.
Examples
# Get the XM accessions from a set of gene ids
locs <- c("LOC101512347")
sapply(locs, function(x) refseq_fromGene (x, sequence = "transcript"), USE.NAMES = FALSE)
# Get the XP accessions from a set of gene ids
locs <- c("LOC101512347")
sapply(locs, function(x) refseq_fromGene (x, sequence = "protein"), USE.NAMES = FALSE)
Get the mRNA or protein accession
Description
refseq_fromGene_action() Returns the mRNA or protein accession from a single GeneID.
Usage
refseq_fromGene_action(GeneID, sequence, retries)
Arguments
GeneID |
A character string of the GeneID. |
sequence |
A character string of the mRNA or protein accession to fetch data from mRNA or protein databases, respectively. |
retries |
A numeric value to control the number of retry attempts to handle 502 errors. |
Value
A character vector containing the mRNA or protein accession corresponding to the especified GeneID.
Author(s)
Jose V. Die
Get the gene symbol
Description
refseq_geneSymbol() Returns the gene symbol from a single Gene id. accession.
Usage
refseq_geneSymbol (id, db)
Arguments
id |
A character string of the transcript or protein id. |
db |
A character string of the "nuccore" or "protein" database. |
Value
A character vector containing the gene symbol corresponding to the especified accession as id.
Author(s)
Jose V. Die
See Also
refseq_protein2RNA to obtain the transcript ids that encode a set of protein ids.
refseq_RNA2protein to obtain the protein ids encoded by a set of transcript ids.
Examples
# Get the gene symbol from a set of transcript accessions
id = c("XM_004487701", "XM_004488493")
sapply(id, function(x) refseq_geneSymbol (x, db = "nuccore"), USE.NAMES = FALSE)
# Get the gene symbol from a set of XP accessions
id = c("XP_004487758")
sapply(id, function(x) refseq_geneSymbol (x, db = "protein"), USE.NAMES = FALSE)
Get the gene symbol
Description
refseq_geneSymbol_action() Returns the gene symbol from a single Gene id. accession.
Usage
refseq_geneSymbol_action (id, db, retries)
Arguments
id |
A character string of the transcript or protein id. |
db |
A character string of the "nuccore" or "protein" database. |
retries |
A numeric value to control the number of retry attempts to handle internet errors. |
Value
A character vector containing the gene symbol corresponding to the especified accession as id.
Author(s)
Jose V. Die
See Also
refseq_protein2RNA to obtain the XM ids that encode a set of XP ids.
refseq_RNA2protein to obtain the XP ids encoded by a set of XM ids.
Get mRNA features
Description
refseq_mRNAfeat() Returns a number of features from a single/multiple mRNA accession(s).
Depending on the function, available accessions in refseqR include RefSeq models with the prefixes XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.
Usage
refseq_mRNAfeat(transcript , feat)
Arguments
transcript |
A character string of the transcript id. |
feat |
A character string of the selected features. Allowed features: 'caption', 'moltype', 'sourcedb', 'updatedate', 'slen', 'organism', 'title'. |
Value
A tibble of summarized results including columns:
caption, mRNA accession
moltype, type of molecule
sourcedb, database (GenBank)
updatedate, date of updated record
slen, molecule length (in bp)
organism
title, sequence description
Author(s)
Jose V. Die
See Also
refseq_fromGene to obtain the transcript or protein accession from a single GeneID accession.
refseq_RNA2protein to obtain the protein accessions encoded by a set of transcript ids.
Examples
# Get several molecular features from a set of mRNA accessions
transcript = c("XM_004487701", "XM_004488493", "XM_004501904")
feat = c("caption", "moltype", "sourcedb", "slen")
refseq_mRNAfeat(transcript ,feat)
Get the transcript accession from the protein accession
Description
refseq_protein2RNA() Returns the transcript accession from a single protein accession.
Depending on the function, available accessions in refseqR include RefSeq models with the prefixes XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.
Usage
refseq_protein2RNA(protein)
Arguments
protein |
A character string of the protein id. |
Value
A character vector containing the transcript ids that encode the protein.
Author(s)
Jose V. Die
See Also
refseq_RNA2protein to obtain the protein ids encoded by a set of transcript ids.
Examples
## Not run:
# Get the transcript id from a single protein accession
protein <- "XP_020244413"
refseq_protein2RNA(protein)
# Get the transcript ids from a set of protein accessions
protein = c("XP_004487758", "XP_004488550")
sapply(protein, function(x) refseq_protein2RNA(x), USE.NAMES = FALSE)
## End(Not run)