This function runs deseq2 on a table genrated with sample2experiment having the covariates added in the names of the columns, separated by the names with underscore.
wrapperDeseq2( output.folder, group = c("sudo", "docker"), experiment.table, log2fc = 1, fdr = 0.1, ref.covar = "0", type = c("gene", "isoform", "mirna"), batch = FALSE )
a character string indicating where the tables generated by samples2experiment are located and were results will be placed
a character string. Two options:
a character string indicating the counts table generated with sample3experiment with addition of covariates
log2fc threshold for differetially expressed genes
covariate to be used as reference
character with three options: gene, isoform, mirna. if gene is used two files are generated for geneset enrichment, the filtered Gene symbols and the background that contains all gene simbols.
logical FALSE, TRUE
Returns a full table of differentially expressed genes (prefix DEfull), a filtered table of differentially expressed genes (prefix DEfiltered) and the normalized counts table (prefix normalized)