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Common Amino Acid-level Transformations

Source: R/am_aa.R
am_aa.Rd

am_aa_pos() separates protein_variant columns into amino acide 'pos', 'ref', and 'alt' columns.

am_aa_pathogenicity() summarizes pathogenicity scores at each protein amino acid position.

Usage

am_aa_pos(tbl)

am_aa_pathogenicity(tbl)

Arguments

tbl

a tibble, usually derived from am_data("aa_substitutions"), `am_data("hg38"), etc. See details.

Value

am_aa_pos() returns the original table with additional columns

  • aa_pos: the position of the protein variant, as an integer().

  • aa_ref: the single-character reference amino acid in the protein variant.

  • aa_alt: the single-character alternate amino acid in the protein variant.

am_aa_pathogenicity() returns a tibble with columns

  • uniprot_id, aa_pos, aa_ref: the UniProt id, and the position and reference amino acid being summarized

  • aa_pathogenicity_n, aa_pathogenicity_mean, aa_pathogenicity_median, aa_pathogenicity_min, aa_pathogenicity_max: the number, average, median, minimum, and maximum of the pathogenicity scores at each amino acid position.

  • aa_pathogenicity_mode: the modal am_class at the amino acid position, as a factor. Tied mode is assigned to lower pathogenicity.

Details

tbl is collect()ed before computation, so all rows must fit into memory.

For am_aa_pos(), tbl must contain a column protein_variant with entries in the form "Q465H", as in the AlphaMissense data.

For am_aa_pathogenicity(), tbl must contain columns uniprot_id, protein_variant, am_pathogenicity and am_class. If am_pos and friends are not already calculated, then am_aa_pos() is called.

Examples


P35557 <-
    am_data("hg38") |>
    filter(uniprot_id %in% "P35557")

am_aa_pos(P35557)
#> # A tibble: 3,085 × 13
#>    CHROM      POS REF   ALT   genome uniprot_id transcript_id    protein_variant
#>    <chr>    <dbl> <chr> <chr> <chr>  <chr>      <chr>            <chr>          
#>  1 chr7  44145139 C     A     hg38   P35557     ENST00000403799… Q465H          
#>  2 chr7  44145139 C     G     hg38   P35557     ENST00000403799… Q465H          
#>  3 chr7  44145140 T     C     hg38   P35557     ENST00000403799… Q465R          
#>  4 chr7  44145140 T     A     hg38   P35557     ENST00000403799… Q465L          
#>  5 chr7  44145140 T     G     hg38   P35557     ENST00000403799… Q465P          
#>  6 chr7  44145141 G     C     hg38   P35557     ENST00000403799… Q465E          
#>  7 chr7  44145141 G     T     hg38   P35557     ENST00000403799… Q465K          
#>  8 chr7  44145143 C     G     hg38   P35557     ENST00000403799… G464A          
#>  9 chr7  44145143 C     T     hg38   P35557     ENST00000403799… G464D          
#> 10 chr7  44145143 C     A     hg38   P35557     ENST00000403799… G464V          
#> # ℹ 3,075 more rows
#> # ℹ 5 more variables: am_pathogenicity <dbl>, am_class <chr>, aa_pos <int>,
#> #   aa_ref <chr>, aa_alt <chr>

am_aa_pos(P35557) |>
    select(
        uniprot_id, POS, REF, ALT, protein_variant,
        starts_with("aa_"), am_pathogenicity, am_class
    ) |>
    arrange(aa_pos)
#> # A tibble: 3,085 × 10
#>    uniprot_id      POS REF   ALT   protein_variant aa_pos aa_ref aa_alt
#>    <chr>         <dbl> <chr> <chr> <chr>            <int> <chr>  <chr> 
#>  1 P35557     44188949 A     C     L2R                  2 L      R     
#>  2 P35557     44188949 A     T     L2Q                  2 L      Q     
#>  3 P35557     44188949 A     G     L2P                  2 L      P     
#>  4 P35557     44188950 G     T     L2M                  2 L      M     
#>  5 P35557     44188950 G     C     L2V                  2 L      V     
#>  6 P35557     44188945 G     C     D3E                  3 D      E     
#>  7 P35557     44188945 G     T     D3E                  3 D      E     
#>  8 P35557     44188946 T     G     D3A                  3 D      A     
#>  9 P35557     44188946 T     C     D3G                  3 D      G     
#> 10 P35557     44188946 T     A     D3V                  3 D      V     
#> # ℹ 3,075 more rows
#> # ℹ 2 more variables: am_pathogenicity <dbl>, am_class <chr>


am_aa_pathogenicity(P35557)
#> # A tibble: 464 × 9
#>    uniprot_id aa_pos aa_ref aa_pathogenicity_n aa_pathogenicity_mean
#>    <chr>       <int> <chr>               <int>                 <dbl>
#>  1 P35557          2 L                       5                0.0818
#>  2 P35557          3 D                       8                0.184 
#>  3 P35557          4 D                       8                0.147 
#>  4 P35557          5 R                       6                0.250 
#>  5 P35557          6 A                       6                0.138 
#>  6 P35557          7 R                       7                0.257 
#>  7 P35557          8 M                       9                0.142 
#>  8 P35557          9 E                       7                0.212 
#>  9 P35557         10 A                       6                0.142 
#> 10 P35557         11 A                       6                0.142 
#> # ℹ 454 more rows
#> # ℹ 4 more variables: aa_pathogenicity_median <dbl>,
#> #   aa_pathogenicity_min <dbl>, aa_pathogenicity_max <dbl>,
#> #   aa_pathogenicity_mode <fct>