readFastqDb - Load sequencing quality scores from a FASTQ file

Description

readFastqDb adds the sequencing quality scores to a data.frame from a FASTQ file. Matching is done by sequence_id.

Usage

readFastqDb(
data,
fastq_file,
quality_offset = -33,
header = c("presto", "asis"),
sequence_id = "sequence_id",
sequence = "sequence",
sequence_alignment = "sequence_alignment",
v_cigar = "v_cigar",
d_cigar = "d_cigar",
j_cigar = "j_cigar",
np1_length = "np1_length",
np2_length = "np2_length",
v_sequence_end = "v_sequence_end",
d_sequence_end = "d_sequence_end",
style = c("num", "ascii", "both"),
quality_sequence = FALSE
)

Arguments

data
data.frame containing sequence data.
fastq_file
path to the fastq file
quality_offset
offset value to be used by ape::read.fastq. It is the value to be added to the quality scores (the default -33 applies to the Sanger format and should work for most recent FASTQ files).
header
FASTQ file header format; one of "presto" or "asis". Use "presto" to specify that the fastq file headers are using the pRESTO format and can be parsed to extract the sequence_id. Use "asis" to skip any processing and use the sequence names as they are.
sequence_id
column in data that contains sequence identifiers to be matched to sequence identifiers in fastq_file.
sequence
column in data that contains sequence data.
sequence_alignment
column in data that contains IMGT aligned sequence data.
v_cigar
column in data that contains CIGAR strings for the V gene alignments.
d_cigar
column in data that contains CIGAR strings for the D gene alignments.
j_cigar
column in data that contains CIGAR strings for the J gene alignments.
np1_length
column in data that contains the number of nucleotides between the V gene and first D gene alignments or between the V gene and J gene alignments.
np2_length
column in data that contains the number of nucleotides between either the first D gene and J gene alignments or the first D gene and second D gene alignments.
v_sequence_end
column in data that contains the end position of the V gene in sequence.
d_sequence_end
column in data that contains the end position of the D gene in sequence.
style
how the sequencing quality should be returned; one of "num", "phred", or "both". Specify "num" to store the quality scores as strings of comma separated numeric values. Use "phred" to have the function return the scores as Phred (ASCII) scores. Use "both" to retrieve both.
quality_sequence
specify TRUE to keep the quality scores for sequence. If false, only the quality score for sequence_alignment will be added to data.

Value

Modified data with additional fields:

  1. quality_alignment: A character vector with ASCII Phred scores for sequence_alignment.
  2. quality_alignment_num: A character vector, with comma separated numerical quality values for each position in sequence_alignment.
  3. quality: A character vector with ASCII Phred scores for sequence.
  4. quality_num: A character vector, with comma separated numerical quality values for each position in sequence.

Examples

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


indexed 0B in  0s, 0B/s
indexed 1.00TB in  0s, 983.19TB/s


indexed 0B in  0s, 0B/s
indexed 1.00TB in  0s, 790.48TB/s

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

See also

maskPositionsByQuality and getPositionQuality