alakazam (version 1.3.0)

getPositionQuality: 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"
)

Value

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

and '_masked'.

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.

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))