QCscores.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/QCscores.R
\name{QCscores}
\alias{QCscores}
\title{Compute Phred scores by position or by read}
\usage{
QCscores(flnm, ln = 301, byPos = FALSE, byRead = FALSE)
}
\arguments{
\item{flnm}{Path of the fastq file to be evaluated.}

\item{ln}{Amplicon length.}

\item{byPos}{Logical indicating if QC by position should be computed.}

\item{byRead}{Logical indicating if QC by read should be computed.
Note that Arguments \code{byPos} and \code{byRead} are mutually exclusive.}
}
\value{
If argument \code{byPos=TRUE}, the function returns a list including
  the following parameters:
  \enumerate{
  \item{\code{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.}
  \item{\code{fvnl}: A vector with normalized read lengths for each Phred quantile.}
  \item{\code{all.ln}: A vector with all read lengths.}}

If argument \code{byRead=TRUE}, the function returns a list including
  the following parameters:
  \enumerate{
  \item{\code{all.ln}: A vector with all read lengths.}
  \item{\code{all.ln30}: A vector with the number of bases below Q30 for each read.}
  \item{\code{all.fnl30}: The result of dividing all.ln30/all.ln, which is the
    fraction of bases below Q30 for each read.}}
}
\description{
Applies \code{\link{FastqStreamer}} over a fastq file and returns quality
  control mesures (Phred scores), either by position or by read.
}
\note{
This function is only defined for correct execution of \code{\link{PoolQCbyPos}} and \code{\link{PoolQCbyRead}}
 functions from the same package.
}
\seealso{
\code{\link{PoolQCbyPos}}, \code{\link{PoolQCbyRead}}, \code{\link{QCplot}}
}
\author{
Alicia Aranda
}