View source: R/map.generator.R
map_generator_dnds | R Documentation |
This function allows you to compute dNdS or DS Maps between a query organism and a set subject organisms stored in the same folder. The corresponding dNdS/DS Maps are then stored in an output folder.
map_generator_dnds(
query_file,
subjects_folder,
output_folder,
eval = "1E-5",
min_qry_coverage_hsp = 50,
min_qry_perc_identity = 30,
ortho_detection = "RBH",
aa_aln_type = "pairwise",
aa_aln_tool = "NW",
codon_aln_tool = "pal2nal",
dnds_est_method = "Comeron",
comp_cores = 1,
progress_bar = TRUE,
sep = ";",
...
)
query_file |
a character string specifying the path to the CDS file of the query organism. |
subjects_folder |
a character string specifying the path to the folder where CDS files of the subject organisms are stored. |
output_folder |
a character string specifying the path to the folder where output dNdS/DS Maps should be stored. |
eval |
a character string specifying the e-value for BLAST based Orthology Inference that is performed in the process of dNdS computations. Please use the scientific notation. |
min_qry_coverage_hsp |
minimum |
min_qry_perc_identity |
minimum |
ortho_detection |
a character string specifying the Orthology Inference method that shall be used to perform
dNdS computations. Possible options are: |
aa_aln_type |
a character string specifying the amino acid alignement type: |
aa_aln_tool |
a character string specifying the program that should be used e.g. "clustalw". |
codon_aln_tool |
a character string specifying the codon alignment tool that shall be used.
Default is |
dnds_est_method |
a character string specifying the dNdS estimation method, e.g. "Comeron","Li", "YN", etc. See Details for all options. |
comp_cores |
number of computing cores that shall be used to perform parallelized computations. |
progress_bar |
should a progress bar be shown. Default is |
sep |
a file separator that is used to store maps as csv file. |
... |
additional parameters that shall be passed to |
Given a query organism and a set of subject organsisms that are stored in the same folder, this function crawls through all subject organsism and as a first step computes the pairwise dNdS Maps between query and subject organsim and as a second step stores the corresponding Map in an output folder.
Hajk-Georg Drost
## Not run:
map_generator_dnds(
query_file = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
subjects_folder = system.file('seqs/map_gen_example', package = 'orthologr'),
aa_aln_type = "pairwise",
aa_aln_tool = "NW",
codon_aln_tool = "pal2nal",
dnds_est_method = "Comeron",
output_folder = "orthologr_dnds_maps",
quiet = TRUE,
comp_cores = 1
)
## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.