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Main Orthology Inference Function

Source: R/orthologs.R
orthologs.Rd

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.

Usage

orthologs(
  query_file,
  subject_files,
  seq_type = "protein",
  outgroup_file = NULL,
  eval = "1E-5",
  format = "fasta",
  ortho_detection = "DIAMOND_RBH",
  sensitivity_mode = "fast",
  max.target.seqs = 10000,
  delete_corrupt_cds = FALSE,
  cdd.path = NULL,
  path = NULL,
  add_params = NULL,
  diamond_params = NULL,
  comp_cores = 1,
  quiet = FALSE,
  clean_folders = FALSE
)

Arguments

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).

seq_type

a character string specifying the sequence type stored in the input file. Options are: "cds", "protein", or "dna". In case of "cds", sequences are translated to protein sequences, in case of "dna", CDS prediction is performed on the corresponding sequences which are subsequently translated to protein sequences. Default is seq_type = "protein".

outgroup_file

currently unused; reserved for future use.

eval

a numeric value specifying the E-Value cutoff for hit detection.

format

a character string specifying the file format of the sequence file, e.g. "fasta". Default is "fasta".

ortho_detection

a character string specifying the orthology inference method to use. Default is ortho_detection = "DIAMOND_RBH" (DIAMOND2 reciprocal best hit). Available methods:

  • "DIAMOND_RBH": DIAMOND2 reciprocal best hit (default; fast, recommended)

  • "DIAMOND_BH": DIAMOND2 best hit

  • "RBH": BLAST reciprocal best hit

  • "BH": BLAST best hit

  • "Orthofinder2": OrthoFinder2 (currently under development)

sensitivity_mode

a character string specifying the DIAMOND2 sensitivity level. Only used when ortho_detection is "DIAMOND_RBH" or "DIAMOND_BH". Options: "faster", "fast" (default), "mid-sensitive", "sensitive", "more-sensitive", "very-sensitive", "ultra-sensitive".

max.target.seqs

a numeric value specifying the number of aligned sequences to keep (DIAMOND2 only). Default is 10000.

delete_corrupt_cds

a logical value indicating whether sequences with corrupt base triplets should be removed from the input file. Default is FALSE.

cdd.path

currently unused; reserved for future use.

path

a character string specifying the path to the orthology inference tool executable.

add_params

a character string specifying additional parameters passed to the orthology inference tool. For DIAMOND2 methods, use diamond_params instead. Default is NULL.

diamond_params

a character string specifying additional parameters passed to DIAMOND2. Only used when ortho_detection is "DIAMOND_RBH" or "DIAMOND_BH". Default is NULL.

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 specifying whether all internal folders storing the output of used programs shall be removed. Default is clean_folders = FALSE.

Value

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.

Details

This function takes sequence files of a query organism and a subject organism and performs orthology inference using a defined orthology inference method to detect orthologous genes.

The following interfaces are implemented in the orthologs function:

DIAMOND2 based methods (recommended):

  • DIAMOND2 reciprocal best hit ("DIAMOND_RBH") — default

  • DIAMOND2 best hit ("DIAMOND_BH")

BLAST based methods:

  • BLAST reciprocal best hit ("RBH")

  • BLAST best hit ("BH")

See also

diamond_rec, diamond_best, blast_rec, dNdS

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{

### DIAMOND2 Reciprocal Best Hit (default)

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")


### DIAMOND2 Best Hit

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 = "DIAMOND_BH")


### BLAST Reciprocal Best Hit

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")


### BLAST Best Hit

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")
} # }