data-raw/aaeg_dmel_orthologs.R

In luciorq/aaegdata: Aedes aegypti Mosquitoes Molecular Information

## data-raw/aaeg_dmel_orthologs.R
## Drosophila melanogaster orthologs from vectorbase - flybase??
## Source: "http://biomart.vectorbase.org/biomart/martview?VIRTUALSCHEMANAME=vb_mart_1806&ATTRIBUTES=alvpagwg_eg_gene.default.homologs.ensembl_gene_id|alvpagwg_eg_gene.default.homologs.dmelanogaster_eg_homolog_ensembl_gene|alvpagwg_eg_gene.default.homologs.dmelanogaster_eg_homolog_associated_gene_name|alvpagwg_eg_gene.default.homologs.dmelanogaster_eg_homolog_orthology_type|alvpagwg_eg_gene.default.homologs.dmelanogaster_eg_homolog_perc_id|alvpagwg_eg_gene.default.homologs.dmelanogaster_eg_homolog_perc_id_r1|alvpagwg_eg_gene.default.homologs.dmelanogaster_eg_homolog_ensembl_peptide&FILTERS=&VISIBLEPANEL=resultspanel"
## data file: "data-raw/vectorbase/aaegl51_vectorbase_dmel_ortolog.csv"


library(dplyr)
aaeg_dmel_orthologs <- readr::read_csv("data-raw/vectorbase/aaegl51_vectorbase_dmel_ortolog.csv")

aaeg_dmel_orthologs <- aaeg_dmel_orthologs %>%
  dplyr::rename(gene = `Gene stable ID`) %>%
  dplyr::rename(dmel_gene = `Drosophila melanogaster gene stable ID`) %>%
  dplyr::rename(dmel_gene_name = `Drosophila melanogaster gene name`) %>%
  dplyr::rename(dmel_homology_type = `Drosophila melanogaster homology type`) %>%
  dplyr::rename(dmel_to_aaeg_identity = `%id. target Drosophila melanogaster gene identical to query gene`) %>%
  dplyr::rename(aaeg_to_dmel_identity = `%id. query gene identical to target Drosophila melanogaster gene`) %>%
  dplyr::rename(dmel_protein = `Drosophila melanogaster protein or transcript stable ID`)

# aaeg_dmel_orthologs %>%
#  dplyr::filter(gene == "AAEL026022")


usethis::use_data(aaeg_dmel_orthologs, overwrite = TRUE, compress = "xz")