Get ENTREZ id from gene SYMBOL

Get ENTREZ id from gene SYMBOL

symbol_to_entrez(.data, .transcript = NULL, .sample = NULL)

Arguments

.data

A tt or tbl object.

.transcript

A character. The name of the gene symbol column.

.sample

The name of the sample column

Value

A tbl

Examples

# This function was designed for data.frame
# Convert from SummarizedExperiment for this example. It is NOT reccomended.

tidybulk::se_mini |> tidybulk() |> as_tibble() |> symbol_to_entrez(.transcript = .feature, .sample = .sample)
#> 'select()' returned 1:many mapping between keys and columns
#> # A tibble: 2,635 × 10
#>    .feature .sample    count Cell.type time  condi…¹  days  dead entre…² entre…³
#>    <chr>    <chr>      <dbl> <chr>     <chr> <lgl>   <dbl> <dbl> <chr>   <chr>  
#>  1 ABCB4    SRR1740034  1035 b_cell    0 d   TRUE        1     1 5244    5244   
#>  2 ABCB9    SRR1740034    45 b_cell    0 d   TRUE        1     1 23457   23457  
#>  3 ACAP1    SRR1740034  7151 b_cell    0 d   TRUE        1     1 9744    9744   
#>  4 ACHE     SRR1740034     2 b_cell    0 d   TRUE        1     1 43      43     
#>  5 ACP5     SRR1740034  2278 b_cell    0 d   TRUE        1     1 54      54     
#>  6 ADAM28   SRR1740034 11156 b_cell    0 d   TRUE        1     1 10863   10863  
#>  7 ADAMDEC1 SRR1740034    72 b_cell    0 d   TRUE        1     1 27299   27299  
#>  8 ADAMTS3  SRR1740034     0 b_cell    0 d   TRUE        1     1 9508    9508   
#>  9 ADRB2    SRR1740034   298 b_cell    0 d   TRUE        1     1 154     154    
#> 10 AIF1     SRR1740034     8 b_cell    0 d   TRUE        1     1 199     199    
#> # … with 2,625 more rows, and abbreviated variable names ¹​condition, ²​entrez.x,
#> #   ³​entrez.y