Extract orthomap from OrthoFinder

This function extract an orthomap from OrthoFinder results given a query species.

of2orthomap(seqname, qt, sl, oc, og)

Arguments

seqname

sequence name of the query species in OrthoFinder

qt

query species taxid

sl

species list as <orthofinder name><tab><species taxid>

oc

specify OrthoFinder <Orthogroups.GeneCounts.tsv>

og

specify OrthoFinder <Orthogroups.tsv>

Value

orthomap object

Author

Kristian K Ullrich

Examples

## of2orthomap
#sl <- tempfile()
#oc <- tempfile()
#og <- tempfile()
#download.file(
#    url=paste0("https://zenodo.org/records/14911022/files/",
#               "ensembl_113_orthofinder_last_species_list.tsv"),
#    destfile=sl)
#download.file(
#    url=paste0("https://zenodo.org/records/14911022/files/",
#               "ensembl_113_orthofinder_last_Orthogroups.GeneCount.tsv.zip"),
#    destfile=oc)
#download.file(
#    url=paste0("https://zenodo.org/records/14911022/files/",
#               "ensembl_113_orthofinder_last_Orthogroups.tsv.zip"),
#    destfile=og)
#query_orthomap <- of2orthomap(seqname="10090.mus_musculus.pep",
#    qt="10090",
#    sl=sl,
#    oc=oc,
#    og=og)