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", "example_quality.tsv", package="alakazam"))
fastq_file <- system.file("extdata", "example_quality.fastq", package="alakazam")
db <- readFastqDb(db, fastq_file, quality_offset=-33)
maskPositionsByQuality(db, min_quality=90, quality_num="quality_alignment_num")

Number of masked sequences: 1

# A tibble: 1 × 37
  sequenc…¹ seque…² rev_c…³ produ…⁴ v_call d_call j_call seque…⁵ germl…⁶ junct…⁷
  <chr>     <chr>   <lgl>   <lgl>   <chr>  <chr>  <chr>  <chr>   <chr>   <chr>  
1 CGCTTTTC… GGCTTT… FALSE   TRUE    IGHV4… IGHD3… IGHJ4… CAGCTG… CAGCTG… TGTGCG…
# … with 27 more variables: junction_aa <chr>, v_cigar <chr>, d_cigar <chr>,
#   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>, …

See also¶

readFastqDb and getPositionQuality