Differencial analysis of expression

bin/DEG.R

+##NAME = "DEG.R"
+##SYNOPSIS = "DEG.R |-f <raw_data_path>/<file_name>.csv -n <normalized_factor_path>/<file_name>.csv -o <results_path> --pool1 lib1,lib2... --pool2 lib3,lib4... --filter true or false --correct "bonferroni" or "BH" --MAplots true or false --alpha 0.05"
+##EXAMPLE = "Rscript --vanilla DEG.R --file './data/count_table.csv' --norm './Normalization/RLE_info.txt' --pool1 'untreated1,untreated2,untreated3,untreated4' --pool2 'treated1,treated2,treated3' --MAplots 'FALSE' --alpha 0.05 --filter TRUE --correct 'BH' --out './results/'"
+##DATE = "03/2016"
+##AUTHORS = "Gaëlle Lefort"
+##KEYWORDS = "RNAseq differentially expressed genes"
+##DESCRIPTION = "DEG.R imports data, converts them into a DGEList object (edgeR), does tests to find differentially expressed genes and produces diagnostic plots." 
+
+
+
 ##################### Differential Analysis Expression #########################
 ################################################################################