Commit ee8ccf15 authored by Etienne Rifa's avatar Etienne Rifa
Browse files

fix deseq2

debug coercing combination in to factor
parent f3f51a1f
Pipeline #40855 passed with stage
in 10 seconds
......@@ -56,9 +56,8 @@ deseq2_fun <- function(data = data, output = "./deseq/", column1 = "", verbose =
# quit()
flog.info('Defining comparison...')
if(comp==""){
fun <- paste('combinaisons <- utils::combn(na.omit(unique(sample_data(data.glom)$',column1,')),2) ',sep='')
fun <- paste('combinaisons <- as.matrix( as.data.frame( utils::combn(na.omit(unique(sample_data(data.glom)$',column1,')),2) ))',sep='')
eval(parse(text=fun))
print(combinaisons)
}else{
comp_list <- unlist(strsplit(comp,","))
# combinaisons <- combn(comp_list,2)
......@@ -71,6 +70,7 @@ deseq2_fun <- function(data = data, output = "./deseq/", column1 = "", verbose =
}
}
print(combinaisons)
flog.info('Done...')
outF = list()
......
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