User Defined Function not working in dplyr pipe - r

Question

I have a dataset with proteins accession numbers (DataGranulomeTidy). I have written a function (extractInfo) in r to scrape some information of those proteins from the ncbi website. The function works as expected when I run it in a short "for" loop.
DataGranulomeTidy <- tibble(GIaccessionNumber = c("29436380", "4504165", "17318569"))
extractInfo <- function(GInumber){
tempPage <- readLines(paste("https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?id=", GInumber, "&db=protein&report=genpept&conwithfeat=on&withparts=on&show-cdd=on&retmode=html&withmarkup=on&tool=portal&log$=seqview&maxdownloadsize=1000000", sep = ""), skipNul = TRUE)
tempPage <- base::paste(tempPage, collapse = "")
Accession <- str_extract(tempPage, "(?<=ACCESSION).{3,20}(?=VERSION)")
Symbol <- str_extract(tempPage, "(?<=gene=\").{1,20}(?=\")")
GeneID <- str_extract(tempPage, "(?<=gov/gene/).{1,20}(?=\">)")
out <- paste(Symbol, Accession, GeneID, sep = "---")
return(out)
}
for(n in 1:3){
print(extractInfo(GInumber = DataGranulomeTidy$GIaccessionNumber[n]))
}
[1] "MYH9--- AAH49849---4627"
[1] "GSN--- NP_000168---2934"
[1] "KRT1--- NP_006112---3848"
When I use the same function in a dplyr pipe I doesn't work and I can't figure our why.
> DataGranulomeTidy %>% mutate(NewVar = extractInfo(.$GIaccessionNumber))
Error in file(con, "r") : argumento 'description' inválido
At this point I could make things work without using the "pipe" operator by using the "for" operator but I would like so much to understand why the function does not work in the dplyr pipe.

Answer 1

It is the cause that your UDF can't treat vector.
vectorized_extractInfo <- Vectorize(extractInfo, "GInumber")
DataGranulomeTidy %>%
mutate(NewVar = vectorized_extractInfo(GIaccessionNumber))

Answer 2

As #cuttlefish44 already pointed out, the problem is that your fun is not a vectorized fun. My approach uses purrr::map_chr. Another option would be to use dplyr::rowwise:
library(tidyverse)
DataGranulomeTidy <- tibble(GIaccessionNumber = c("29436380", "4504165", "17318569"))
extractInfo <- function(GInumber){
tempPage <- readLines(paste("https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?id=", GInumber, "&db=protein&report=genpept&conwithfeat=on&withparts=on&show-cdd=on&retmode=html&withmarkup=on&tool=portal&log$=seqview&maxdownloadsize=1000000", sep = ""), skipNul = TRUE)
tempPage <- base::paste(tempPage, collapse = "")
Accession <- str_extract(tempPage, "(?<=ACCESSION).{3,20}(?=VERSION)")
Symbol <- str_extract(tempPage, "(?<=gene=\").{1,20}(?=\")")
GeneID <- str_extract(tempPage, "(?<=gov/gene/).{1,20}(?=\">)")
out <- paste(Symbol, Accession, GeneID, sep = "---")
return(out)
}
DataGranulomeTidy %>% mutate(NewVar = map_chr(GIaccessionNumber, extractInfo))
#> # A tibble: 3 x 2
#> GIaccessionNumber NewVar
#> <chr> <chr>
#> 1 29436380 MYH9--- AAH49849---4627
#> 2 4504165 GSN--- NP_000168---2934
#> 3 17318569 KRT1--- NP_006112---3848
Created on 2020-04-17 by the reprex package (v0.3.0)

Answer 3

There is a rentrez package for NCBI queries, for example:
library(rentrez)
protein <- entrez_summary("protein", id = 29436380)
protein$caption
# [1] "AAH49849"
links <- entrez_link(dbfrom = "protein", id = 29436380, db = "gene")
links$links$protein_gene
# [1] "4627"
gene <- entrez_summary("gene", id = links$links$protein_gene)
gene$name
# [1] "MYH9"
Wrap this up into a function, then we don't need to mess about with regex.