# #设置,包括= FALSE --------------------------------------------------- knitr: opts_chunk美元集(崩溃= TRUE,评论= " # > ",dpi = 100 ) ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- 库(微波激射器)库(rtracklayer) #创建路径< -系统使用缺氧微波激射器对象数据集。file("extdata"， file.path("MATS_output")， package = "maser") hypoxia <- maser(path, c(" hypoxia 0h"， " hypoxia 24h")) #移除低覆盖事件hypoxia_filt <- filterByCoverage(hypoxia, avg_reads = 5) ## ---- warning =FALSE, message =FALSE, echo=FALSE---------------------------- knitr::kable(head(availableFeaturesUniprotKB()， 10)) ## ---- warning =FALSE, message =FALSE ---------------------------------------- ## Ensembl GTF annotation gtf_path <- system. system. bat)文件(“extdata file.path(“GTF”、“Ensembl85_examples.gtf.gz”),包=“微波激射器”)ens_gtf < - rtracklayer:: import.gff (gtf_path ) ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- # 检索特定基因剪接事件srsf6_events < geneEvents (hypoxia_filt, SRSF6) srsf6_events # #——警告= FALSE,消息= FALSE ---------------------------------------- # 地图记录剪接事件srsf6_mapped < - mapTranscriptsToEvents (srsf6_events,ens_gtf ) ## ---- 警告= FALSE,消息= FALSE, eval = FALSE ---------------------------- # 头(注释(SE srsf6_mapped。 ")) ## ---- 警告= FALSE,消息= FALSE,回声= FALSE ---------------------------- knitr: kable(头(注释(SE srsf6_mapped。 ")) ) ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- # 与蛋白质功能注释剪接事件srsf6_annot < mapProteinFeaturesToEvents (srsf6_mapped c(“Domain_and_Sites”、“拓扑”),=“类别 ") ## ---- 警告= FALSE,消息= FALSE, eval = FALSE ---------------------------- # 头(注释(SE srsf6_annot。 ")) ## ---- 警告= FALSE,消息= FALSE,回声= FALSE ---------------------------- knitr: kable(头(注释(SE srsf6_annot。 ")) ) ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- # plotUniprotKBFeatures情节拼接事件,转录和蛋白质特性(srsf6_mapped,“本身”,event_id = 33209, gtf = ens_gtf特性= c(“域”,“链”),show_transcripts = TRUE ) ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- ripk2_events < - geneEvents (hypoxia_filt RIPK2) ripk2_mapped < - mapTranscriptsToEvents (ripk2_events ens_gtf) ripk2_annot < mapProteinFeaturesToEvents (ripk2_mapped追踪= c(“Domain_and_Sites”),由= "范畴 ") ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- plotUniprotKBFeatures (ripk2_annot类型=“本身”,event_id = 14319,特点= c(“域”、“绑定”,“act-site”),gtf = ens_gtf变焦= FALSE, show_transcripts = TRUE ) ## ---- 回声= FALSE -------------------------------------------------------------- sessionInfo ()