## ----message = FALSE---------------------------------------------------------- library(BRGenomics) data("PROseq") ## ----------------------------------------------------------------------------- ps_list <- lapply(1:6, function(i) PROseq[seq(i, length(PROseq), 6)]) names(ps_list) <- c("A_rep1", "A_rep2", "B_rep1", "B_rep2", "C_rep1", "C_rep2") ## ----------------------------------------------------------------------------- ps_list[1:2] names(ps_list) ## ----------------------------------------------------------------------------- data("txs_dm6_chr4") ## ----------------------------------------------------------------------------- dds <- getDESeqDataSet(ps_list, txs_dm6_chr4, gene_names = txs_dm6_chr4$gene_id, ncores = 1) dds ## ----------------------------------------------------------------------------- getDESeqResults(dds, contrast.numer = "B", contrast.denom = "A", quiet = TRUE, ncores = 1) ## ----------------------------------------------------------------------------- comparison_list <- list(c("B", "A"), c("C", "A"), c("C", "B")) dsres <- getDESeqResults(dds, comparisons = comparison_list, quiet = TRUE, ncores = 1) names(dsres) dsres$C_vs_B