read.gene.mapping.info.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/momentum_routines.R
\name{read.gene.mapping.info}
\alias{read.gene.mapping.info}
\title{read in detailed molecular mapping info from hdf5 file as written out by "-d" option of velocyto.py}
\usage{
read.gene.mapping.info(fname, cell.clusters = NULL,
  internal.priming.info = NULL, min.exon.count = 10,
  n.cores = defaultNCores(), engine = "hdf5r")
}
\arguments{
\item{fname}{name of the hdf5 detailed molecular mapping (debug) file, written out by velocyto.py}

\item{cell.clusters}{optional cell cluster factor}

\item{internal.priming.info}{optionall internal priming info, as produced by find.ip.sites() function}

\item{min.exon.count}{minimal total (dataset-wide) number of molecules for an exon to be considered expressed}

\item{n.cores}{number of cores to use}

\item{engine}{use either h5 or hdf5r to read the input hdf5 file}
}
\value{
a list containing gene structural information data structure ($gene.df, with el,il, nex,nipconc,nipdisc columns corresponding to the log10 exonic length, intronic length, number of exons, numebr of internal concordant and discordant priming sites, respectively), and $info tables from the hdf5 file with an additional per-cluster entry $cluster.feature.counts table showing per-feature (rows) per-cluster (column) molecule counts (if cell.clusters are not supplied $info$cluster.feauture.counts will contain one column, 'all' giving dataset-wide counts)
}
\description{
read in detailed molecular mapping info from hdf5 file as written out by "-d" option of velocyto.py
}