| Title: | A Pipeline to Define Gene Families in Legumes and Beyond |
| Version: | 1.0.11 |
| Description: | A pipeline with high specificity and sensitivity in extracting proteins from the RefSeq database (National Center for Biotechnology Information). Manual identification of gene families is highly time-consuming and laborious, requiring an iterative process of manual and computational analysis to identify members of a given family. The pipelines implements an automatic approach for the identification of gene families based on the conserved domains that specifically define that family. See Die et al. (2018) <doi:10.1101/436659> for more information and examples. |
| Depends: | R (≥ 3.4.0) |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| LazyData: | true |
| Imports: | rentrez (≥ 1.2.1), stringr (≥ 1.4.0), dplyr (≥ 0.8.0.1), httr (≥ 1.4.0), utils, curl (≥ 3.3) |
| Suggests: | knitr, rmarkdown |
| URL: | https://github.com/NCBI-Hackathons/GeneHummus |
| BugReports: | https://github.com/NCBI-Hackathons/GeneHummus/issues |
| RoxygenNote: | 6.1.1 |
| NeedsCompilation: | no |
| Packaged: | 2019-04-04 22:19:22 UTC; josedie |
| Author: | Jose V. Die  [aut,
cre],
Moamen M. Elmassry [ctb],
Kimberly H. LeBlanc [ctb],
Olaitan I. Awe [ctb],
Allissa Dillman [ctb],
Ben Busby [aut] |
| Maintainer: | Jose V. Die <jose.die@uco.es> |
| Repository: | CRAN |
| Date/Publication: | 2019-04-04 22:30:03 UTC |
genehummus: A pipeline to define gene families in Legumes and beyond
Description
genehummus is a pipeline with high specificity and sensitivity in extracting proteins from the RefSeq database (NCBI).
Author(s)
Jose V. Die jose.die@uco.es, Moamen M. Elmassry, Kimberly H. LeBlanc, Olaitan I. Awe, Allissa Dillman, Ben Busby
See Also
see the preprint in BioRvix
Compute the total number of accession proteins per species
Description
Summarizes a dataframe of protein ids and return the total number of accessions per organism.
Usage
accessions_by_spp(my_accessions)
Arguments
my_accessions |
A data frame with accession protein ids and organisms |
Value
A data.frame of summarized results including columns:
organism, taxonomic species
N.seqs, total number of sequences
Author(s)
Jose V. Die
See Also
getAccessions to create the data frame with acession
id and organism for each protein identifier.
Examples
my_prots = data.frame(accession = c("XP_014620925", "XP_003546066",
"XP_025640041", "XP_019453956", "XP_006584791", "XP_020212415",
"XP_017436622", "XP_004503803", "XP_019463844"),
organism = c("Glycine max", "Glycine max", "Arachis hypogaea",
"Lupinus angustifolius", "Glycine max", "Cajanus cajan",
"Vigna angularis", "Cicer arietinum", "Lupinus angustifolius"))
accessions_by_spp(my_prots)
Extract the accession ids (XP accession) for a given organism
Description
Filter a dataframe of protein ids and return the accessions for a given species or organism.
Usage
accessions_from_spp(my_accessions, spp)
Arguments
my_accessions |
A data frame with accession protein ids and organisms |
spp |
A string with the scientific name of the species or organism. |
Value
A string vector with protein accession (XP accession, RefSeq database)
Author(s)
Jose V. Die
See Also
getAccessions to create the data frame with accession
id and organism for each protein identifier.
Examples
my_prots = data.frame(accession = c("XP_014620925", "XP_003546066",
"XP_025640041", "XP_019453956", "XP_006584791", "XP_020212415",
"XP_017436622", "XP_004503803", "XP_019463844"),
organism = c("Glycine max", "Glycine max", "Arachis hypogaea",
"Lupinus angustifolius", "Glycine max", "Cajanus cajan",
"Vigna angularis", "Cicer arietinum", "Lupinus angustifolius"))
accessions_from_spp(my_prots, "Glycine max")
Get acessions and organism for each protein identifier
Description
Core function used by getAccessions.
Usage
accessions_warning(protein_ids)
Arguments
protein_ids |
A string vector containing protein identifiers. |
Author(s)
Jose V. Die
Get architecture identifiers for the conserved domains
Description
Parses SPARCLE database (NCBI) and extract electronic identifiers for each conserved domain.
Usage
archids_warning(gene_family)
Arguments
gene_family |
A string with conserved domain(s). |
Author(s)
Jose V. Die
Get the protein identifiers
Description
Extract the protein identifier for the given taxonomic species, which are hosted by the RefSeq database (NCBI).
Usage
extract_proteins(targets, taxonIds)
Arguments
targets |
A string with the electronic links for the SPARCLE architecture. |
taxonIds |
A string with the taxonomic species identifiers; legume species (by default). |
Details
First, get the protein ids from RefSeq database. Then, extract only the ids for the selected taxonomic species (by default, legume species).
Author(s)
Jose V. Die
Filter the protein architectures based on conserved domains
Description
Parse the architecture identifiers and extract those that contain, at least, those selected in the filter.
Usage
filterArch_ids(archs_ids, filter)
Arguments
archs_ids |
A string with the architecture identifiers that contain, at least, one of the conserved domains defining the gene family. |
filter |
A string with the domains (and order) that are required (at least) for the proteins to have. |
Value
the architecture identifiers from all the potential protein architectures
defined by getArch_ids that contain, at least, the conserved
domains explicitily show by the filter.
Author(s)
Jose V. Die
See Also
Examples
## Not run:
archs_ids <- getArch_ids("pfam02362")
my_filter <- c("B3_DNA", "Auxin_resp")
filterArch_ids(archs_ids, my_filter)
## End(Not run)
Filter protein architectures based on conserved domains
Description
Parse the architecture identifiers and extract those that contain, at least, the conserved domaind selected as filter.
Usage
filterarchids_warning(archs_ids, filter)
Arguments
archs_ids |
A string with the architecture identifiers. |
filter |
A string with the domains as filter. |
Author(s)
Jose V. Die
Get the acessions ids and the organism for each protein identifier
Description
The getAccessions function parses the protein page for each identifier
and extracts the accession id (usually referred as XP accession in the RefSeq
database) and the organism given by the scientific name.
The accessions_by_spp and accessions_from_spp functions are
convenient filters for further cleaning of getAccessions by giving
the total number of XP accessions per species or extracting the XP
accessions for a given species, respectively.
Usage
getAccessions(protein_ids)
Arguments
protein_ids |
A string vector containing protein identifiers. |
Value
A data.frame of protein ids including columns:
accession
organism
Author(s)
Jose V. Die
See Also
accessions_by_spp to summarize the total number of
accession proteins per species.
accessions_from_spp to filter the accession ids for
a given species
Examples
prot_ids <- c("593705262", "1379669790", "357520645", "1150156484")
getAccessions(prot_ids)
Get the potential architecture identifiers for the conserved domains
Description
Parses the SPARCLE database (NCBI) and extract the electronic identifiers for each conserved domain.
Usage
getArch_ids(gene_family)
Arguments
gene_family |
A string with the conserved domain(s) defining the gene family. The domains have to be shown in the same order appearing in the sequences. |
Value
the architectures identifiers for each of the conserved domains.
Author(s)
Jose V. Die
Examples
arf <- c("pfam06507")
getArch_ids(arf)
Get the description label for a protein architecture identifier
Description
Parses the architecture identifiers and extract their corresponding labels.
Usage
getArch_labels(arch_ids)
Arguments
arch_ids |
A string with the architecture electronic identifiers. |
Value
print out the description label for the candidate architectures that contain the proteins we are looking for.
Author(s)
Jose V. Die
See Also
filterArch_ids
Examples
filtered_archids <- c("12034188", "12034184")
getArch_labels(filtered_archids)
Get the RefSeq protein identifiers for the given taxonomic species
Description
Parse the RefSeq database using protein architecture identifiers (SPARCLE dabatse) and extract the protein ids. for the selected taxonomic species.
Usage
getProteins_from_tax_ids(arch_ids, taxonIds)
Arguments
arch_ids |
A string with the electronic links for the SPARCLE. |
taxonIds |
A vector string with taxonomy ids; Legume species available in RefSeq, by default. |
Value
RefSeq protein identifiers for selected species.
Author(s)
Jose V. Die
Examples
filtered_archids <- c("12034184")
medicago <- c(3880)
getProteins_from_tax_ids(filtered_archids, medicago)
Get the protein identifiers for a given architecture
Description
Parse the RefSeq database and extract all the protein identifiers that have a given architecture.
Usage
getProtlinks(archs_ids)
Arguments
archs_ids |
A string with the architecture identifiers (SPARCLE database, NCBI) |
Author(s)
Jose V. Die
Get the electronic architecture for a conserved domain
Description
Parses the SPARCLE database (NCBI) and extract the electronic links for a given conserved domain.
Usage
getSparcleArchs(CD)
Arguments
CD |
A string with the conserved domain(s) |
Author(s)
Jose V. Die
Get the species name from the description sequence
Description
Parse a string vector with sequence descriptions (title and species) and extract the species name.
Usage
get_spp(description)
Arguments
description |
A string vector with the sequence description (title and species). |
Value
for each sequence description, extract the species name.
Author(s)
Jose V. Die
Get description label for a protein architecture identifier
Description
Parses the architecture identifier and extract the corresponding labels.
Usage
labels_warning(arch_ids)
Arguments
arch_ids |
A string with the architecture electronic identifiers. |
Author(s)
Jose V. Die
NCBI taxonomy ids for the legume family
Description
Taxonomy identifier for about 10,000 legume species
Usage
data(legumesIds)
Format
a numeric vector with 10.009 elements
Source
Taxonomy identifiers for Fabaceae species (Taxonomy databse, NCBI).
ARF proteins per legume specie
Description
XP accessions for the Auxin Response Factor gene family in the Legume Legume taxonomy (NCBI RefSeq database, as of SEP 2018).
Usage
data(my_legumes)
Format
a list of length 10 with 563 elements.
1. chickpea
2. medicago
3. soybean
4. arachis_duranensis
5. arachis_ipaensis
6. cajanus
7. vigna_angulata
8. vigna_radiata
9. phaseolus
10. lupinus
Source
Protein identifiers for Fabaceae species (RefSeq databse, NCBI).
Get RefSeq protein identifiers for the given taxonomic species
Description
Parse the RefSeq database using protein architecture identifiers and
extract protein ids. for selected taxonomic species. Core function used
by getProteins_from_tax_ids.
Usage
proteins_warning(arch_ids, taxonIds)
Arguments
arch_ids |
A string with the electronic links for the SPARCLE. |
taxonIds |
A vector string with taxonomy ids. |
Author(s)
Jose V. Die
Build a list containing N elements per element list
Description
Split a vector into N elements, so that each element contains a given length.
Usage
sizeIds
Format
An object of class numeric of length 1.
Author(s)
Jose V. Die