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#' Get acessions and organism for each protein identifier
#'
#' Core function used by \code{\link{getAccessions}}.
#'
#' @importFrom rentrez entrez_post entrez_summary extract_from_esummary
#' @importFrom dplyr %>% mutate select
#'
#' @usage
#' accessions_warning(protein_ids)
#'
#' @param protein_ids A string vector containing protein identifiers.
#'
#' @author Jose V. Die
accessions_warning <-
function(protein_ids) {
vals = c()
if(length(protein_ids) < 300 ) {
upload <- entrez_post(db="protein", id=protein_ids) #create a web_history object
prot_summ = entrez_summary(db="protein", web_history=upload)
vals = as.character((extract_from_esummary(prot_summ, c("caption","title"))))
} else {
protein_ids = subsetIds(protein_ids, sizeIds)
for(i in seq(length(protein_ids))) {
upload <- entrez_post(db="protein", id=protein_ids[[i]]) #create a web_history object
prot_summ = entrez_summary(db="protein", web_history=upload)
vals = c(vals, as.character((extract_from_esummary(prot_summ, c("caption","title")))))
}
}
vals_df = data.frame(matrix(unlist(vals),
nrow = length(vals)/2, byrow = T), #/2 bc 2 cols
row.names = colnames(vals),
stringsAsFactors = F)
colnames(vals_df) = c("accession", "desc")
vals_df
sci_name = sapply(vals_df$desc, function(x) get_spp(x), USE.NAMES = FALSE)
vals_df %>%
mutate(organism = sci_name) %>%
select(accession, organism) -> my_data
my_data
}
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