diff --git a/session_4/session_4.Rmd b/session_4/session_4.Rmd index 46b7df47494c322b1dd67bb7db802e55b0c3af42..a5fa1ecc50a184688c7573171be5fe8e36d3847a 100644 --- a/session_4/session_4.Rmd +++ b/session_4/session_4.Rmd @@ -560,7 +560,20 @@ Open the csv file using the `read_csv2()` function. The file is located at "http ```{r read_csv2} tab <- read_csv2("http://perso.ens-lyon.fr/laurent.modolo/R/session_4/EWang_Tibialis_DEGs_GRCH37-87_GSE86356.csv") -expr_DM1 +tab ``` </p> </details> + +To make a Volcano plot, displaying different information about the significativity of the variation thanks to the colors, we will have to make a series of modifications on this table. + +We will have to create : + +- a column 'sig' : it indicates if the gene is significant ( TRUE or FALSE ). +**Thresholds :** baseMean > 20 and padj < 0.05 and abs(log2FoldChange) >= 1.5 + +- a column 'UpDown' : it indicates if the gene is Up regulated or Down regulated. + + + +