## ----样式，echo = false，结果='asis'--------------------------------------------------------------------------- BiocStyle :: Markdown（css.files = C（'Custom.css'））## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------＃if（！sireseenamespace（“ Biocmanager）“，悄悄= true））＃install.packages（“ biocmanager”）＃＃＃biocmanager :: install（c（“ epitxdb”，“ epitxdb”，“ epitxdb.hs.hg38”））## ----结果=“ hide”，include = true，messages = false，警告= false -------------------库（EpitXDB）库（Epitxdb.hs.hg38）## ----------------------------------------------------------------------------------------------------------------------------------------------- etdb <- EpiTxDb.Hs.hg38.snoRNAdb() etdb ## ---------------------------------------------------------------------------------------------------------------键形（ETDB）列（ETDB）head（键（etdb，“ modid”））select（etdb，keys =“ 1”，列= c（“ modname”，“ modtype”，“ modtype”，“”modstart“，“ modstrand”，“ snname”，“ rxGeneName”，“ spectype”，“ specgenName”），keytype =“ modid”）## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------物种（ETDB）生物（ETDB）SEQlevels（ETDB）## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- modifications(etdb, columns = c("mod_id","mod_type","mod_name”，“ rx_geneName”，“ spec_geneName”，“ ref_type”，“ ref”），filter = list（mod_id = 1：3））## -------------------------------------------------------------------------------------------------------------------------------------------------------------＃按序列名称拆分，通常是transcipt标识符修改（etdb，by =“ seqnames”）＃split修改type oftificationby by（etdb，by by =“ modtype”）## ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- echo = FALSE------------------------------------------------------------ suppressPackageStartupMessages({ library(TxDb.Hsapiens.UCSC.hg38.knownGene) library(BSgenome.Hsapiens.UCSC.hg38) }) ## ---- eval = FALSE------------------------------------------------------------ # library(TxDb.Hsapiens.UCSC.hg38.knownGene) # library(BSgenome.Hsapiens.UCSC.hg38) ## ----------------------------------------------------------------------------- txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene seqlevels(txdb) <- "chr1" bs <- BSgenome.Hsapiens.UCSC.hg38 etdb <- EpiTxDb.Hs.hg38.RMBase() tx <- exonsBy(txdb) mod <- modifications(etdb, filter = list(sn_name = "chr1")) length(mod) ## ----------------------------------------------------------------------------- mod_tx <- shiftGenomicToTranscript(mod, tx) length(mod_tx) ## ----------------------------------------------------------------------------- mod_tx <- split(mod_tx,seqnames(mod_tx)) names <- Reduce(intersect,list(names(mod_tx),names(tx))) # Getting the corresponding 5'-UTR and 3'-UTR annotations fp <- fiveUTRsByTranscript(txdb) tp <- threeUTRsByTranscript(txdb) tx <- tx[names] mod_tx <- mod_tx[names] fp_m <- match(names,names(fp)) fp_m <- fp_m[!is.na(fp_m)] tp_m <- match(names,names(tp)) tp_m <- tp_m[!is.na(tp_m)] fp <- fp[fp_m] tp <- tp[tp_m] # Getting lengths of transcripts, 5'-UTR and 3'-UTR tx_lengths <- sum(width(tx)) fp_lengths <- rep(0L,length(tx)) names(fp_lengths) <- names fp_lengths[names(fp)] <- sum(width(fp)) tp_lengths <- rep(0L,length(tx)) names(tp_lengths) <- names tp_lengths[names(tp)] <- sum(width(tp)) # Rescale modifications # CDS start is at position 1L and cds end at position 1000L from <- IRanges(fp_lengths+1L, tx_lengths - tp_lengths) to <- IRanges(1L,1000L) mod_rescale <- rescale(mod_tx, to, from) # Construct result data.frame rel_pos <- data.frame(mod_type = unlist(mcols(mod_rescale,level="within")[,"mod_type"]), rel_pos = unlist(start(mod_rescale))) rel_pos <- rel_pos[rel_pos$rel_pos < 1500 & rel_pos$rel_pos > -500,] ## ----------------------------------------------------------------------------- library(ggplot2) ggplot(rel_pos[rel_pos$mod_type %in% c("m6A","m1A","Y"),], aes(x = rel_pos, colour = mod_type)) + geom_density() ## ----------------------------------------------------------------------------- sessionInfo()