View source: R/orthologs_lnc.R View source: R/orthologs.lnc.R
orthologs_lnc | R Documentation |
This function takes nucleotide or protein sequences for a set of organisms and performs orthology inference to detect orthologous genes within the given organisms based on selected orthology inference programs.
This function takes nucleotide or protein sequences for a set of organisms and performs orthology inference to detect orthologous genes within the given organisms based on selected orthology inference programs.
orthologs_lnc(
query_file,
subject_file,
task = "blastn",
eval = "1E-5",
ortho_detection = "RBH",
max.target.seqs = 10000,
output.path = getwd(),
comp_cores = 1,
path = NULL
)
orthologs_lnc(
query_file,
subject_file,
task = "blastn",
eval = "1E-5",
ortho_detection = "RBH",
max.target.seqs = 10000,
output.path = getwd(),
comp_cores = 1,
path = NULL
)
query_file |
a character string specifying the path to the sequence file of interest (query organism). |
subject_file |
a character string specifying the paths to the sequence files of interest (subject organisms). |
task |
nucleotide search task option. Options are:
|
eval |
a numeric value specifying the E-Value cutoff for BLAST hit detection. |
ortho_detection |
a character string specifying the orthology inference method that shall be performed to detect orthologous genes. Options are:
|
max.target.seqs |
a numeric value specifying the number of aligned sequences to keep. Please be aware that max.target.seqs selects best hits based on the database entry and not by the best e-value. See details here: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty833/5106166 . |
output.path |
path to which output shall be stored. |
comp_cores |
a numeric value specifying the number of cores to be used for multicore computations. |
path |
a character string specifying the path to the corresponding orthology inference tool. For "BH" and "RBH": path to BLAST, "PO": path to ProteinOrtho 5.07, "OrthoMCL": path to OrthoMCL. |
This function takes sequence files of a query organism and a subject organism and performs orthology inference using a defined orthology inference method to dectect orthologous genes.
The following interfaces are implemented in the orthologs
function:
BLAST based methods:
BLAST best hit (BH)
BLAST reciprocal best hit (RBH)
This function takes sequence files of a query organism and a subject organism and performs orthology inference using a defined orthology inference method to dectect orthologous genes.
The following interfaces are implemented in the orthologs
function:
BLAST based methods:
BLAST best hit (BH)
BLAST reciprocal best hit (RBH)
A data.table storing the query_ids of orthologous genes in the first column, the subject_ids of orthologous genes in the second column and the amino acid sequences in the third column.
A data.table storing the query_ids of orthologous genes in the first column, the subject_ids of orthologous genes in the second column and the amino acid sequences in the third column.
Hajk-Georg Drost
BLAST: http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
ProteinOrtho: https://www.bioinf.uni-leipzig.de/Software/proteinortho/
BLAST: http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
ProteinOrtho: https://www.bioinf.uni-leipzig.de/Software/proteinortho/
blast_rec
, dNdS
blast_rec
, dNdS
## Not run:
### BLAST Reciprocal Best Hit
# perform orthology inference using BLAST reciprocal best hit
# and fasta sequence files storing protein sequences
orthologs.lnc(query_file = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
subject_file = system.file('seqs/ortho_lyra_cds.fasta', package = 'orthologr'),
ortho_detection = "RBH")
### BLAST Best Hit
# perform orthology inference using BLAST best hit
# and fasta sequence files storing protein sequences
orthologs.lnc(query_file = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
subject_file = system.file('seqs/ortho_lyra_cds.fasta', package = 'orthologr'),
ortho_detection = "BH")
# multicore version
orthologs.lnc(query_file = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
subject_file = system.file('seqs/ortho_lyra_cds.fasta', package = 'orthologr'),
ortho_detection = "RBH",
comp_cores = 2)
## End(Not run)
## Not run:
### BLAST Reciprocal Best Hit
# perform orthology inference using BLAST reciprocal best hit
# and fasta sequence files storing protein sequences
orthologs.lnc(query_file = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
subject_file = system.file('seqs/ortho_lyra_cds.fasta', package = 'orthologr'),
ortho_detection = "RBH")
### BLAST Best Hit
# perform orthology inference using BLAST best hit
# and fasta sequence files storing protein sequences
orthologs.lnc(query_file = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
subject_file = system.file('seqs/ortho_lyra_cds.fasta', package = 'orthologr'),
ortho_detection = "BH")
# multicore version
orthologs.lnc(query_file = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
subject_file = system.file('seqs/ortho_lyra_cds.fasta', package = 'orthologr'),
ortho_detection = "RBH",
comp_cores = 2)
## End(Not run)
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