Nothing
#' Get statistics about coverage per sample
#'
#' @param project.directory Path to project directory. Each sample should have its own subdirectory
#'
#' @return coverage.by.sample.statistics Data frame with coverage statistics per sample
#'
#'
get.coverage.by.sample.statistics <- function(project.directory) {
### INPUT TESTS ###########################################################
if( !is.character(project.directory) || length(project.directory) > 1 ) {
stop('project.directory must be a string.');
}
if( !file.exists(project.directory) ) {
error.message <- paste('Directory', project.directory, 'does not exist');
stop(error.message);
}
### MAIN ##################################################################
# gather data from individual files
total.coverage.statistics <- process.total.coverage.statistics(project.directory);
coverage.report.data <- process.coverage.reports(project.directory);
# merge – this has to be done pairwise
# does the sample order have to match Ros' ?
coverage.by.sample.statistics <- merge(
total.coverage.statistics,
coverage.report.data,
by = "sample.id",
all = TRUE
);
return(coverage.by.sample.statistics);
}
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