map_ids_uniprot

Access to uniprot web API. For more detail see https://www.uniprot.org/help/uploadlists

map_ids_uniprot(
  data,
  ID_col = "UniprotID",
  from = "ACC+ID",
  to = "P_ENTREZGENEID",
  format = "tab"
)

Arguments

data	data
ID_col	column name containing id's
from	id type
to	id type
format	in which format to return the mapping

See also

Other id_mapping: map_ids_2ways(), map_ids_annotationHub(), mapthe()

Examples

library(tidyverse)
fc_estimates <- prora::exampleContrastData

filtered_dd <- get_UniprotID_from_fasta_header(fc_estimates, idcolumn = "protein_Id")
# debug(map_ids_uniprot)
map_ids_uniprot( filtered_dd )
#> No encoding supplied: defaulting to UTF-8.
#> Rows: 3719 Columns: 2
#> -- Column specification --------------------------------------------------------
#> Delimiter: "\t"
#> chr (1): From
#> dbl (1): To
#> 
#> i Use `spec()` to retrieve the full column specification for this data.
#> i Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> # A tibble: 3,855 x 4
#>    UniprotID P_ENTREZGENEID protein_Id            estimate
#>    <chr>     <chr>          <chr>                    <dbl>
#>  1 Q9BRQ0    90780          sp|Q9BRQ0|PYGO2_HUMAN   0.514 
#>  2 P13645    3858           sp|P13645|K1C10_HUMAN  -2.33  
#>  3 Q9Y4F1    10160          sp|Q9Y4F1|FARP1_HUMAN   0.240 
#>  4 P14550    10327          sp|P14550|AK1A1_HUMAN  -0.360 
#>  5 P61011    6729           sp|P61011|SRP54_HUMAN  -0.0803
#>  6 Q96NC0    153527         sp|Q96NC0|ZMAT2_HUMAN  -1.38  
#>  7 Q15417    1266           sp|Q15417|CNN3_HUMAN    0.108 
#>  8 P31350    6241           sp|P31350|RIR2_HUMAN   -0.468 
#>  9 O60664    10226          sp|O60664|PLIN3_HUMAN   1.83  
#> 10 O95639    10898          sp|O95639|CPSF4_HUMAN   0.199 
#> # ... with 3,845 more rows