maskPositionsByQuality: Mask sequence positions with low quality

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

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".

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")

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.