alakazam (version 1.2.1)

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"
)

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".

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.

See Also

readFastqDb and getPositionQuality

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")