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) forsequence
.
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", "test_seq.tsv", package="alakazam"))
Error: ‘’ does not exist in current working directory (‘/home/edelaron/git/Immcantation/alakazam’).
fastq_file <- system.file("extdata", "test_seq.fastq", package="alakazam")
db <- readFastqDb(db, fastq_file, quality_offset=-33)
Warning:failed to read sequences, returns NULLError in attr(DNA, “QUAL”) <- QUAL: attempt to set an attribute on NULL
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