QCscores: Compute Phred scores by position or by read

In aliafdz/QApckg: Quality assessment for Miseq data derived from viral sequencing

Compute Phred scores by position or by read

Description

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

Usage

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

Arguments

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 byPos and byRead are mutually exclusive.

Value

If argument byPos=TRUE, the function returns a list including the following parameters:

1. 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.

2. fvnl: A vector with normalized read lengths for each Phred quantile.

3. all.ln: A vector with all read lengths.

If argument byRead=TRUE, the function returns a list including the following parameters:

1. all.ln: A vector with all read lengths.

2. all.ln30: A vector with the number of bases below Q30 for each read.

3. all.fnl30: The result of dividing all.ln30/all.ln, which is the fraction of bases below Q30 for each read.

Note

This function is only defined for correct execution of PoolQCbyPos and PoolQCbyRead functions from the same package.

Author(s)

Alicia Aranda

See Also

PoolQCbyPos, PoolQCbyRead, QCplot

aliafdz/QApckg documentation built on June 2, 2022, 10:29 a.m.