## ---- message = FALSE--------------------------------------------------------- library(BRGenomics) library(Biostrings) ## ----------------------------------------------------------------------------- # get path to included 2bit file sfile <- system.file("extdata", "dm6_chr4chrM.2bit", package = "BRGenomics") ## ----------------------------------------------------------------------------- seq_chr4 <- import(sfile) seq_chr4 ## ----------------------------------------------------------------------------- data("txs_dm6_chr4") txs_pr <- promoters(txs_dm6_chr4, 0, 100) ## ----------------------------------------------------------------------------- seq_txs_pr <- getSeq(TwoBitFile(sfile), txs_pr) seq_txs_pr ## ----------------------------------------------------------------------------- RNAStringSet(seq_txs_pr) suppressWarnings(translate(seq_txs_pr)) oligonucleotideFrequency(seq_txs_pr[1:5], width = 1) oligonucleotideFrequency(seq_txs_pr[1:5], width = 2) ## ----------------------------------------------------------------------------- tss_seq <- getSeq(TwoBitFile(sfile), promoters(txs_dm6_chr4, 4, 4)) tsspwm <- PWM(tss_seq) tsspwm