View source: R/generate_ortholog_tables_all.R
generate_ortholog_tables_all | R Documentation |
Given an input folder storing dNdS tables generated by dNdS
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 BLAST hit to represent either a gene locus (e.g. the splice variant of the gene locus with lowest e-value) or the best BLAST hit for a splice varaint.
generate_ortholog_tables_all(
dNdS_folder,
annotation_file_query,
annotation_folder_subject,
output_folder,
output_type = "gene_locus",
format = c("gtf", "gtf")
)
dNdS_folder |
file path to folder storing a |
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
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