QCscores | R Documentation |

Applies `FastqStreamer`

over a fastq file and returns quality
control mesures (Phred scores), either by position or by read.

QCscores(flnm, ln = 301, byPos = FALSE, byRead = FALSE)

`flnm` |
Path of the fastq file to be evaluated. |

`ln` |
Amplicon length. |

`byPos` |
Logical indicating if QC by position should be computed. |

`byRead` |
Logical indicating if QC by read should be computed.
Note that Arguments |

If argument `byPos=TRUE`

, the function returns a list including
the following parameters:

`fvnq`

: A matrix with Phred quality scores across each nucleotide base in the reads. Columns indicate base position and rows indicate 0.05, 0.25, 0.5, 0.75 and 0.95 Phred quantiles.`fvnl`

: A vector with normalized read lengths for each Phred quantile.`all.ln`

: A vector with all read lengths.

If argument `byRead=TRUE`

, the function returns a list including
the following parameters:

`all.ln`

: A vector with all read lengths.`all.ln30`

: A vector with the number of bases below Q30 for each read.`all.fnl30`

: The result of dividing all.ln30/all.ln, which is the fraction of bases below Q30 for each read.

This function is only defined for correct execution of `PoolQCbyPos`

and `PoolQCbyRead`

functions from the same package.

Alicia Aranda

`PoolQCbyPos`

, `PoolQCbyRead`

, `QCplot`

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