Description Usage Arguments Author(s) See Also Examples
View source: R/import_dnds_across_multiple_species.R
Given an input folder storing dnds tables generated by dnds_across_multiple_species
and
annotation files stored in an annotation folder for the query (one annotation file) and subject species in gtf
or gff
file format, this function selects the best DIAMOND hit to represent either a gene locus (e.g. the splice variant of the gene locus with lowest e-value) or the best DIAMOND hit for a splice varaint.
1 2 3 4 5 6 7 8 | import_dnds_across_multiple_species(
dnds_output_folder,
annotation_file_query,
annotation_folder_subject,
output_folder,
output_type = "gene_locus",
format = c("gtf", "gtf")
)
|
dnds_output_folder |
file path to folder storing |
annotation_file_query |
file path to the annotation file of the query species in |
annotation_folder_subject |
file path to a folder storing the annotation files of the subject species in |
output_folder |
file path to a folder in which orthologs tables shall be stored. |
output_type |
type of ortholog table that shall be printed out (or stored in a variable). Available options are:
|
format |
a vector of length 2 storing the annotation file formats of the query annotation file and subject annotation file: either |
Hajk-Georg Drost
dnds_across_multiple_species
, dnds
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | ## Not run:
# running dnds across several species using DIAMOND executable
# path '/opt/miniconda3/bin/'
dnds_across_multiple_species(
query = system.file('seqs/ortho_thal_cds.fasta', package = 'homologr'),
subjects_folder = system.file('seqs/map_gen_example', package = 'homologr'),
diamond_exec_path = "/opt/miniconda3/bin/",
aa_aln_type = "pairwise",
aa_aln_tool = "NW",
codon_aln_tool = "pal2nal",
dnds_estimation = "Li",
output_folder = file.path(tempdir(), "homologr_dnds_maps"),
quiet = TRUE,
cores = 1
)
# Import dnds tables by gene locus and splice varaint for a set of species
import_dnds_tables <- import_dnds_across_multiple_species(
dnds_output_folder = "homologr_dnds_maps",
annotation_file_query = "system.file('seqs/ortho_thal.gtf', package = 'homologr')",
annotation_folder_subject = system.file('seqs/plants_subject_files', package = 'homologr'),
output_folder = file.path(tempdir(), "homologr_dnds_maps", "orthologs_tables"),
output_type = "gene_locus",
format = c("gtf", "gtf"))
# look at results
lapply(import_dnds_tables, head)
## End(Not run)
|
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