maskSequences - 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
Value¶
A tibble with masked sequence in sequence_masked column, as well as other columns.
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
See also¶
maskCodons, pwalign::pairwiseAlignment.