intPhred {girafe} | R Documentation

## Extract integer Phred score values from FastQ data

### Description

Function to extract integer Phred score values from FastQ data.

### Usage

    intPhred(x, method="Sanger", returnType="list")

### Arguments

`x` | object of class `ShortReadQ`; which contains read sequences and quality scores; usually read in from a Fastq files.
`method` | string; one of 'Sanger', 'Solexa' or 'previousSolexa'. See details below.
`returnType` | string; in which format should the result be returned, either as a 'list' or as a 'matrix'.

### Details

There are different standards for encoding read qualities in Fastq files. The 'Sanger' format encodes a Phred quality score from 0 to 93 using ASCII 33 to 126. The current 'Solexa'/llumina format (1.3 and higher) encodes a Phred quality score from 0 to 40 using ASCII 64 to 104. The 'previous Solexa'/Illumina format (1.0) encodes a custom Solexa/Illumina quality score from -5 to 40 using ASCII 59 to 104. This custom Solexa quality score is approximately equal to the Phred scores for high qualities, but differs in the low quality range.

### Value

If `returnType` is equal to ‘list’: A list of integer Phred quality values of the same length as the number of reads in the object `x`.

If `returnType` is equal to ‘matrix’: A matrix of integer Phred quality values. The number of rows is the number of reads in the object `x`. The number of columns is the maximum length (width) over all reads in object `x`. The last entries for reads that are shorter than this maximum width are 'NA'.

### Author(s)

Joern Toedling

### References

http://maq.sourceforge.net/fastq.shtml

### See Also

`ShortReadQ-class`, `readFastq`

### Examples

      exDir <- system.file("extdata", package="girafe")
      ra  <- readFastq(dirPath=exDir, pattern=
                "aravinSRNA_23_plus_adapter_excerpt.fastq")
      ra.quals <- intPhred(ra, method="Sanger",
                           returnType="matrix")
      ra.qmed  <- apply(ra.quals, 2, median)
      if (interactive())
         plot(ra.qmed, type="h", ylim=c(0,42), xlab="Base postion",
              ylab="Median Phred Quality Score", lwd=2, col="steelblue")

[Package girafe version 1.44.0 Index]