maskPositionsByQuality - Mask sequence positions with low quality

Description¶

maskPositionsByQuality will replace positions that have a sequencing quality score lower that min_quality with an "N" character.

Usage¶

maskPositionsByQuality(
data,
min_quality = 70,
sequence = "sequence_alignment",
quality_num = "quality_alignment_num"
)

Arguments¶

data

data.frame containing sequence data.

min_quality

minimum quality score. Positions with sequencing quality less than min_qual will be masked.

sequence

column in data with sequence data to be masked.

quality_num

column in data with quality scores (a string of numeric values, comma separated) that can be used to mask sequence.

Value¶

Modified data data.frame with an additional field containing quality masked sequences. The name of this field is created concatenating the sequence name and "_masked".

Examples¶

db <- airr::read_rearrangement(system.file("extdata", "test_seq.tsv", package="alakazam"))

Error: ‘’ does not exist in current working directory (‘/home/edelaron/git/Immcantation/alakazam’).

fastq_file <- system.file("extdata", "test_seq.fastq", package="alakazam")
db <- readFastqDb(db, fastq_file, quality_offset=-33)

Warning:failed to read sequences, returns NULLError in attr(DNA, “QUAL”) <- QUAL: attempt to set an attribute on NULL

maskPositionsByQuality(db, min_quality=90, quality_num="quality_alignment_num")

Number of masked sequences: 1

# A tibble: 1 × 40
  sequence_id       sequence  rev_comp productive v_call d_call j_call sequence_alignment germline_alignment junction junction_aa v_cigar d_cigar
  <chr>             <chr>     <lgl>    <lgl>      <chr>  <chr>  <chr>  <chr>              <chr>              <chr>    <chr>       <chr>   <chr>  
1 CGCTTTTCGGATTGGAA GGCTTTCT… FALSE    TRUE       IGHV4… IGHD3… IGHJ4… CAGCTGCACCTGCAGGA… CAGCTGCAGCTGCAGGA… TGTGCGA… CARGTDLVTG… 93S8=1… 403S9N…
# ℹ 27 more variables: j_cigar <chr>, stop_codon <lgl>, vj_in_frame <lgl>, locus <chr>, junction_length <int>, np1_length <int>,
#   np2_length <int>, v_sequence_start <int>, v_sequence_end <int>, v_germline_start <int>, v_germline_end <int>, d_sequence_start <int>,
#   d_sequence_end <int>, d_germline_start <int>, d_germline_end <int>, j_sequence_start <int>, j_sequence_end <int>, j_germline_start <int>,
#   j_germline_end <int>, consensus_count <int>, duplicate_count <int>, c_call <chr>, quality_num <chr>, quality <chr>,
#   quality_alignment_num <chr>, quality_alignment <chr>, sequence_alignment_masked <chr>

See also¶

readFastqDb and getPositionQuality