Commit 7bdf1b93 authored by Claire Hoede's avatar Claire Hoede
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Differencial analysis of expression

parent d69159a9
##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 #########################
################################################################################
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