getPositionQuality: Get a data.frame with sequencing qualities per position

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

Get a data.frame with sequencing qualities per position

Description

getPositionQuality takes a data.frame with sequence quality scores in the form of a strings of comma separated numeric values, split the quality scores values by ",", and returns a data.frame with the values for each position.

Usage

getPositionQuality(
  data,
  sequence_id = "sequence_id",
  sequence = "sequence_alignment",
  quality_num = "quality_alignment_num"
)

Arguments

data	data.frame containing sequence data.
sequence_id	column in data with sequence identifiers.
sequence	column in data with sequence data.
quality_num	column in data with quality scores (as strings of numeric values, comma separated) for sequence.

Value

data with one additional field with masked sequences. The name of this field is created concatenating sequence and '_masked'.

See Also

readFastqDb and maskPositionsByQuality

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)
head(getPositionQuality(db))

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