maskSequences {dowser}

maskSequences Mask codons split by insertions in V gene

Description

maskSequences Mask codons split by insertions in V gene

Usage

maskSequences(
  data,
  sequence_id = "sequence_id",
  sequence = "sequence",
  sequence_alignment = "sequence_alignment",
  v_sequence_start = "v_sequence_start",
  v_sequence_end = "v_sequence_end",
  v_germline_start = "v_germline_start",
  v_germline_end = "v_germline_end",
  junction_length = "junction_length",
  keep_alignment = FALSE,
  keep_insertions = FALSE,
  mask_codons = TRUE,
  mask_cdr3 = TRUE,
  nproc = 1
)

Arguments

data

BCR data table

sequence_id

sequence id column

sequence

input sequence column (query)

sequence_alignment

aligned (IMGT-gapped) sequence column (subject)

v_sequence_start

V gene start position in sequence

v_sequence_end

V gene end position in sequence

v_germline_start

V gene start position in sequence_alignment

v_germline_end

V gene end position in sequence_alignment

junction_length

name of junction_length column

keep_alignment

store alignment of query and subject sequences?

keep_insertions

return removed insertion sequences?

mask_codons

mask split codons?

mask_cdr3

mask CDR3 sequences?

nproc

number of cores to use

Details

Performs global alignment of sequence and sequence_alignment, masking codons in sequence_alignment that are split by insertions (see examples) masking_note notes codon positions in subject_alignment sequence that were masked, if found. subject_alignment contains subject sequence aligned to query sequence (only if keep_alignment=TRUE) query_alignment contains query sequence aligned to subject sequence (only if keep_alignment=TRUE) sequence_masked will be NA if frameshift or alignment error detected. This will be noted insertions column will be returned if keep_insertions=TRUE, contains a comma-separated list of each <position in query alignment>-<sequence>. See example. in masking_note.

Value

A tibble with masked sequence in sequence_masked column, as well as other columns.

See Also

maskCodons, Biostrings::pairwiseAlignment.