Skip to contents

Label mutations

Source: R/label_mutations.R
label_mutations.Rd

For each data point, label a mutation as "ref", "alt", "ins", or "del".

  • Data points that have more reference (REF) than alternate (ALT) calls will be labeled as "ref".

  • Mutations whose REF and ALT calls are both one base pair and who have more ALT calls than REF calls will be labeled as "alt".

  • Mutations whose REF and ALT calls differ in length and have more ALT calls than REF calls will be labeled as "ins".

  • Mutations whose REF and ALT calls differ in length and have more REF calls than ALT calls will be labeled as "del".

Usage

label_mutations(.data, .before = NULL, .after = NULL)

Arguments

.data

The data set containing REF and ALT calls.

.before, .after

[Experimental] <tidy-select> Optionally, control where new columns should appear (the default is to add to the right hand side). See relocate() for more details.

Examples

data <- tibble::tribble(
  ~sample, ~pos, ~ref, ~alt, ~ref_umi_count, ~alt_umi_count, ~coverage,
  "S1", "1049838", "A", "G", 54, 10, 64,
  "S2", "801498", "G", "A", 15, 0, 15,
  "S3", "625403", "T", "C", 0, 15, 15,
  "S4", "748165", "GA", "G", 2, 18, 20,
  "S5", "487199", "G", "ATC", 0, 10, 10
)

label_mutations(data)
#> # A tibble: 5 × 8
#>   sample pos     ref   alt   ref_umi_count alt_umi_count coverage ans_der_indel
#>   <chr>  <chr>   <chr> <chr>         <dbl>         <dbl>    <dbl> <chr>        
#> 1 S1     1049838 A     G                54            10       64 ref          
#> 2 S2     801498  G     A                15             0       15 ref          
#> 3 S3     625403  T     C                 0            15       15 alt          
#> 4 S4     748165  GA    G                 2            18       20 del          
#> 5 S5     487199  G     ATC               0            10       10 ins          
label_mutations(data, .after = alt)
#> # A tibble: 5 × 8
#>   sample pos     ref   alt   ans_der_indel ref_umi_count alt_umi_count coverage
#>   <chr>  <chr>   <chr> <chr> <chr>                 <dbl>         <dbl>    <dbl>
#> 1 S1     1049838 A     G     ref                      54            10       64
#> 2 S2     801498  G     A     ref                      15             0       15
#> 3 S3     625403  T     C     alt                       0            15       15
#> 4 S4     748165  GA    G     del                       2            18       20
#> 5 S5     487199  G     ATC   ins                       0            10       10
label_mutations(data, .before = pos)
#> # A tibble: 5 × 8
#>   sample ans_der_indel pos     ref   alt   ref_umi_count alt_umi_count coverage
#>   <chr>  <chr>         <chr>   <chr> <chr>         <dbl>         <dbl>    <dbl>
#> 1 S1     ref           1049838 A     G                54            10       64
#> 2 S2     ref           801498  G     A                15             0       15
#> 3 S3     alt           625403  T     C                 0            15       15
#> 4 S4     del           748165  GA    G                 2            18       20
#> 5 S5     ins           487199  G     ATC               0            10       10