maskPositionsByQuality - Mask sequence positions with low quality
maskPositionsByQuality will replace positions that
have a sequencing quality score lower that
min_quality with an
maskPositionsByQuality( data, min_quality = 70, sequence = "sequence_alignment", quality_num = "quality_alignment_num" )
data.framecontaining sequence data.
- minimum quality score. Positions with sequencing quality
min_qualwill be masked.
- column in
datawith sequence data to be masked.
- column in
datawith quality scores (a string of numeric values, comma separated) that can be used to mask
data data.frame with an additional field containing
quality masked sequences. The name of this field is created
sequence name and
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)
Error in alakazam::checkColumns(data, check_cols): object ‘db’ not found
maskPositionsByQuality(db, min_quality=90, quality_num="quality_alignment_num")
Error in checkColumns(data, required_cols): object ‘db’ not found