Commit d652afa4 authored by Etienne Rifa's avatar Etienne Rifa
Browse files

verbose modes aggregate

parent 64f00514
Pipeline #38545 passed with stage
in 10 seconds
......@@ -9,7 +9,7 @@
#' @param mgseq Path to metagenomeseq results folder
#' @param column1 Column name of factor to test (among sample_variables(data))
#' @param column2 Column name on which table were splitted
#' @param verbose Verbose level. (1: quiet, 3: verbal)
#' @param verbose Verbose level. (1: quiet, 2: print infos, 3: print infos + debug)
#' @param rank Taxonomy rank to merge features that have same taxonomy at a certain taxonomic rank (among rank_names(data), or 'ASV' for no glom)
#' @param comp Comparison to test. Comma separated and comparisons are informed with a tilde (A~C,A~B,B~C). If empty, test all combination.
#' @param returnval Boolean for function to return values.
......@@ -34,10 +34,15 @@ aggregate_fun <- function(data = data, metacoder = NULL, deseq = NULL, mgseq = N
if(verbose == 3){
invisible(flog.threshold(DEBUG))
} else {
}
if(verbose == 2){
invisible(flog.threshold(INFO))
}
if(verbose == 1){
invisible(flog.threshold(ERROR))
}
if(!dir.exists(output)){
dir.create(output,recursive=T )
}
......
......@@ -33,7 +33,7 @@ aggregate_fun(
\item{column2}{Column name on which table were splitted}
\item{verbose}{Verbose level. (1: quiet, 3: verbal)}
\item{verbose}{Verbose level. (1: quiet, 2: print infos, 3: print infos + debug)}
\item{rank}{Taxonomy rank to merge features that have same taxonomy at a certain taxonomic rank (among rank_names(data), or 'ASV' for no glom)}
......
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