Given a indel and its sequence context, categorize it

This function is primarily for internal use, but we export it to document the underlying logic.

Usage

categorize_1_justified_indel(
  context,
  ins_or_del,
  ins_or_del_seq,
  pos,
  chrom = NULL,
  genomic_pos = NULL
)

Arguments

context

The sequence surrounding the indel PRIOR to the insertion or deletion.

ins_or_del

A single character, with "i" denoting an insertion and "d" denoting a deletion.

ins_or_del_seq

The sequence that was inserted or deleted.

pos

For deletions, the 1-based position of the start of the deleted sequence; for insertions, the position immediately to the right of where the insertion occurs.

chrom

Optional chromosome name; used only to enrich error messages when the deletion sequence does not match the context.

genomic_pos

Optional genomic position; used only to enrich error messages when the deletion sequence does not match the context.

Value

A string that is the canonical representation of the given deletion type. Return NA and raise a warning if there is an un-normalized representation of the deletion of a repeat unit. See FindDelMH for details. (This seems to be very rare.)

Details

See https://github.com/steverozen/ICAMS/blob/v3.0.9-branch/data-raw/PCAWG7_indel_classification_2021_09_03.xlsx for additional information on deletion mutation classification.

This function first handles deletions in homopolymers, then handles deletions in simple repeats with longer repeat units (e.g. CACACACA), and if the deletion is not in a simple repeat, looks for microhomology.

Examples

simplify = function(ll) unlist(ll[c("COSMIC_83", "Koh_89", "Koh_476")])
categorize_1_justified_indel("GGAAAGG", "d", ins_or_del_seq = "A", pos = 3) # "DEL:T:1:2"
#> $ins_or_del
#> [1] "d"
#> 
#> $pre
#> [1] "C"
#> 
#> $ins_or_del_seq
#> [1] "T"
#> 
#> $post
#> [1] "C"
#> 
#> $L
#> [1] 1
#> 
#> $U_seq
#> [1] "T"
#> 
#> $U
#> [1] 1
#> 
#> $U_seq_count_in_indel_seq
#> [1] 1
#> 
#> $indel_str_count_in_ref
#> [1] 3
#> 
#> $R
#> [1] 3
#> 
#> $R_outside_ins_or_del_seq
#> [1] 2
#> 
#> $mh
#> [1] 0
#> 
#> $short_visual
#> [1] "<A>[AA]"
#> 
#> $long_visual
#> [1] "GG <A>[AA] GG"
#> 
#> $unit
#> [1] "A"
#> 
#> $unit_length
#> [1] 1
#> 
#> $internal_rep
#> [1] ""
#> 
#> $internal_reps
#> [1] 0
#> 
#> $spacer
#> [1] ""
#> 
#> $spacer_length
#> [1] 0
#> 
#> $prime3_rep
#> [1] "AA"
#> 
#> $prime3_reps
#> [1] 2
#> 
#> $original_reps
#> [1] 3
#> 
#> $COSMIC_83
#> [1] "DEL:T:1:2"
#> 
#> $Koh_89
#> [1] "C[Del(T):R(1,4)]C"
#> 
#> $Koh_476
#> [1] "C[Del(T):R3]C"
#> 
categorize_1_justified_indel("GGAAAGG", "d", ins_or_del_seq = "A", pos = 4) # "DEL:T:1:2"
#> $ins_or_del
#> [1] "d"
#> 
#> $pre
#> [1] "C"
#> 
#> $ins_or_del_seq
#> [1] "T"
#> 
#> $post
#> [1] "T"
#> 
#> $L
#> [1] 1
#> 
#> $U_seq
#> [1] "T"
#> 
#> $U
#> [1] 1
#> 
#> $U_seq_count_in_indel_seq
#> [1] 1
#> 
#> $indel_str_count_in_ref
#> [1] 2
#> 
#> $R
#> [1] 2
#> 
#> $R_outside_ins_or_del_seq
#> [1] 2
#> 
#> $mh
#> [1] 0
#> 
#> $short_visual
#> [1] "<A>[A]"
#> 
#> $long_visual
#> [1] "GGA <A>[A] GG"
#> 
#> $unit
#> [1] "A"
#> 
#> $unit_length
#> [1] 1
#> 
#> $internal_rep
#> [1] ""
#> 
#> $internal_reps
#> [1] 0
#> 
#> $spacer
#> [1] ""
#> 
#> $spacer_length
#> [1] 0
#> 
#> $prime3_rep
#> [1] "A"
#> 
#> $prime3_reps
#> [1] 1
#> 
#> $original_reps
#> [1] 2
#> 
#> $COSMIC_83
#> [1] "DEL:T:1:1"
#> 
#> $Koh_89
#> [1] "C[Del(T):R(1,4)]T"
#> 
#> $Koh_476
#> [1] "C[Del(T):R2]T"
#> 
simplify(
  categorize_1_justified_indel("TTATT", "d", ins_or_del_seq = "A", pos = 3))
#>           COSMIC_83              Koh_89             Koh_476 
#>         "DEL:T:1:0" "A[Del(T):R(1,4)]A"     "A[Del(T):R1]A" 
simplify(
  categorize_1_justified_indel("TTATATAT", "d", ins_or_del_seq = "TATA", pos = 2))
#>         COSMIC_83            Koh_89           Koh_476 
#>      "DEL:MH:4:3" "Del(4,5):M(3,4)"         "Del4:M3" 
simplify(
  categorize_1_justified_indel("TTATATAT", "d", ins_or_del_seq = "TATAT", pos = 2))
#>          COSMIC_83             Koh_89            Koh_476 
#> "DEL:repeats:5+:0"       "Del(5,):R1"    "Del5:U(2,):R1"