calculate mean Phred score from an ASCII encoded phred string

FASTQ and BAM store per base qualities as an ASCII string. Accessory methods in e.g. ShortRead allow for a sum of the numeric encoded scores; this is not corrected for the log/linear so scores are synthetically boosted

  • this simple method performs mean on the character level data ...

qualToMeanQ(qstr)

Arguments

qstr

is an ASCII encoded Phred quality score

Value

mean phred scaled q-value

Examples

qualToMeanQ('ABCDEF')
#> [1] 34.16954