orthologs | 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.
orthologs(
query_file,
subject_files,
seq_type = "protein",
outgroup_file = NULL,
eval = "1E-5",
format = "fasta",
ortho_detection = "RBH",
delete_corrupt_cds = FALSE,
cdd.path = NULL,
path = NULL,
add_params = NULL,
comp_cores = 1,
quiet = FALSE,
clean_folders = FALSE
)
query_file |
a character string specifying the path to the sequence file of interest (query organism). |
subject_files |
a character string specifying the paths to the sequence files of interest (subject organisms). Different orthology inference methods can detect orthologs using multiple subject organisms, e.g. "OrthoMCL", and "PO" (ProteinOrtho). |
seq_type |
a character string specifying the sequence type stored in the input file.
Options are are: "cds", "protein", or "dna". In case of "cds", sequence are translated to protein sequences,
in case of "dna", cds prediction is performed on the corresponding sequences which subsequently are
translated to protein sequences. Default is |
outgroup_file |
a character string specifying the paths to the sequence files of interest (outgroup organisms).
This argument is only used by |
eval |
a numeric value specifying the E-Value cutoff for BLAST hit detection. |
format |
a character string specifying the file format of the sequence file, e.g. "fasta", "gbk". Default is "fasta". |
ortho_detection |
a character string specifying the orthology inference method that shall be performed
to detect orthologous genes. Default is |
delete_corrupt_cds |
a logical value indicating whether sequences with corrupt base triplets should be removed from the input |
cdd.path |
path to the cdd database folder (specify when using |
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. |
add_params |
a character string specifying additional parameters that shall be handed to the orthology inference method (tool).
Default is |
comp_cores |
a numeric value specifying the number of cores to be used for multicore computations. |
quiet |
a logical value specifying whether a successful interface call shall be printed out. |
clean_folders |
a boolean value spefiying whether all internall folders storing the output of used programs
shall be removed. Default is |
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)
DELTA-BLAST reciprocal best hit (DELTA)
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_rec
, dNdS
## Not run:
### BLAST Best Hit
# perform orthology inference using BLAST best hit
# and fasta sequence files storing protein sequences
orthologs(query_file = system.file('seqs/ortho_thal_aa.fasta', package = 'orthologr'),
subject_files = system.file('seqs/ortho_lyra_aa.fasta', package = 'orthologr'),
seq_type = "protein",
ortho_detection = "BH")
### BLAST Reciprocal Best Hit
# perform orthology inference using BLAST reciprocal best hit
# and fasta sequence files storing protein sequences
orthologs(query_file = system.file('seqs/ortho_thal_aa.fasta', package = 'orthologr'),
subject_files = system.file('seqs/ortho_lyra_aa.fasta', package = 'orthologr'),
seq_type = "protein",
ortho_detection = "RBH")
# multicore version
orthologs(query_file = system.file('seqs/ortho_thal_aa.fasta', package = 'orthologr'),
subject_files = system.file('seqs/ortho_lyra_aa.fasta', package = 'orthologr'),
seq_type = "protein",
ortho_detection = "RBH",
comp_cores = 2)
## End(Not run)
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