phredScoreStringToInt: Convert Phred Quality Score Strings to Integers

Description Usage Arguments Details Value Examples

Description

Turn the cryptic Phred quality scores from FASTQ files, etc., into integers

Usage

1
phredScoreStringToInt(txt, scoreType = "Phred33")

Arguments

txt

character vector of Phred quality score strings

scoreType

type of offset used for the ASCII coded scores. Currently, only 'Phred33' and 'Phred66' are supported.

Details

Most efficient for strings of equal length.

Value

an integer matrix with NR rows and NC columns, where NR = length(txt) and NC = max(nchar(txt)). Each element is the Phred score of one DNA base call.

Examples

1
  phredScoreStringToInt( c( "_ABBBB&&.#$&", "IIIIIIIIIIII"))

robertdouglasmorrison/DuffyTools documentation built on Dec. 14, 2018, 3:05 p.m.