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"
)

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’.

Examples¶

db <- airr::read_rearrangement(system.file("extdata", "example_quality.tsv", package="alakazam"))

indexed 0B in  0s, 0B/s
indexed 1.00TB in  0s, 1.00PB/s


indexed 0B in  0s, 0B/s
indexed 1.00TB in  0s, 739.08TB/s

fastq_file <- system.file("extdata", "example_quality.fastq", package="alakazam")
db <- readFastqDb(db, fastq_file, quality_offset=-33)
head(getPositionQuality(db))

Warning:NAs introduced by coercion

  position quality_alignment_num       sequence_id nt
1        1                    90 CGCTTTTCGGATTGGAA  C
2        2                    90 CGCTTTTCGGATTGGAA  A
3        3                    90 CGCTTTTCGGATTGGAA  G
4        4                    90 CGCTTTTCGGATTGGAA  C
5        5                    90 CGCTTTTCGGATTGGAA  T
6        6                    90 CGCTTTTCGGATTGGAA  G

See also¶

readFastqDb and maskPositionsByQuality