## ----eval = FALSE------------------------------------------------------------- # # install.packages("BiocManager") # BiocManager::install("BRGenomics") ## ----eval = FALSE------------------------------------------------------------- # # install.packages("remotes") # remotes::install_github("mdeber/BRGenomics@R3") ## ----message=FALSE------------------------------------------------------------ library(BRGenomics) ## ----------------------------------------------------------------------------- data("PROseq") PROseq ## ----------------------------------------------------------------------------- data("txs_dm6_chr4") txs_dm6_chr4 ## ----------------------------------------------------------------------------- length(txs_dm6_chr4) ## ----------------------------------------------------------------------------- txs_dm6_chr4[2] ## ----------------------------------------------------------------------------- tx4 <- txs_dm6_chr4[c(1, 10, 200, 300)] tx4 ## ----------------------------------------------------------------------------- width(tx4) ## ----------------------------------------------------------------------------- mcols(tx4) ## ----------------------------------------------------------------------------- mcols(tx4)[, 2] mcols(tx4)[, "gene_id"] tx4$gene_id tx4_names <- tx4$tx_name tx4_names ## ----------------------------------------------------------------------------- tx4$gene_id[1] ## ----------------------------------------------------------------------------- mcols(tx4) <- mcols(tx4)[, -1] tx4 ## ----------------------------------------------------------------------------- names(mcols(tx4)) <- "gene_id" tx4 ## ----------------------------------------------------------------------------- tx4$tx_name <- tx4_names tx4 ## ----------------------------------------------------------------------------- tx4$gene_id[1] <- "gene1" tx4$tx_name <- 1:4 tx4 ## ----------------------------------------------------------------------------- start(tx4) ## ----------------------------------------------------------------------------- tx4_tss <- resize(tx4, width = 1, fix = "start") tx4_tss start(tx4_tss) ## ----------------------------------------------------------------------------- mcols(tx4) <- NULL tx4