% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/read_pathoscope_data.R
\name{read_pathoscope_data}
\alias{read_pathoscope_data}
\title{Reads the data from PathoScope reports and returns a list of
final guess relative abundance and count data}
\usage{
read_pathoscope_data(
  input_dir = ".",
  pathoreport_file_suffix = "-sam-report.tsv",
  use.input.files = FALSE,
  input.files.path.vec = NULL,
  input.files.name.vec = NULL
)
}
\arguments{
\item{input_dir}{Directory where the tsv files from PathoScope are located}

\item{pathoreport_file_suffix}{PathoScope report files suffix}

\item{use.input.files}{whether input dir to pathoscope files
or directly pathoscope files}

\item{input.files.path.vec}{vector of pathoscope file paths}

\item{input.files.name.vec}{vector of pathoscope file names}
}
\value{
List of final guess relative abundance and count data
}
\description{
Reads the data from PathoScope reports and returns a list of
final guess relative abundance and count data
}