# #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) #路径缺氧数据路径< -系统。文件(“extdata file.path(“MATS_output”),包=“微波激射器”)缺氧< -微波激射器(路径,c(“缺氧0 h”、“缺氧24小时”),ftype = " ReadsOnTargetAndJunctionCounts ") ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- 缺氧# #——警告= FALSE,消息= FALSE, eval = FALSE ---------------------------- # (总结(缺氧、类型=“SE”)[1:8 ]) ## ---- 警告= FALSE,消息= FALSE,回声= FALSE ---------------------------- knitr: kable(头(总结(缺氧,类型=“SE”)[1:8 ]) ) ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- hypoxia_filt < - filterByCoverage(缺氧,avg_reads = 5 ) ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- hypoxia_top < - topEvents (hypoxia_filt,富兰克林·德兰诺·罗斯福= 0.05,deltaPSI = 0.1) hypoxia_top # #——警告= FALSE,消息= FALSE ---------------------------------------- hypoxia_mib2 < - geneEvents (hypoxia_filt,基因=“MIB2”,罗斯福= 0.05,deltaPSI = 0.1)打印(hypoxia_mib2 ) ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- 微波激射器:显示器(SE hypoxia_mib2。 ") ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- plotGenePSI (hypoxia_mib2类型=“本身”,show_replicates = TRUE ) ## ---- 警告= FALSE,消息= FALSE, fig.small = TRUE ---------------------- 火山(hypoxia_filt,富兰克林·德兰诺·罗斯福= 0.05,deltaPSI = 0.1, type = " ") ## ---- 警告= FALSE,消息= FALSE,fig.small = TRUE ---------------------- dotplot (hypoxia_top type = " ") ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- ## 运用GTF注释gtf_path < -系统。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SRSF6剪接事件srsf6_events < - geneEvents (hypoxia_filt基因=“SRSF6”,罗斯福= 0.05,deltaPSI = 0.1) # #规格影响成绩单和PSI水平plotTranscripts (srsf6_events类型=“本身”,event_id = 33209, gtf = ens_gtf变焦= FALSE,show_PSI = TRUE ) ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- stat2_events < - geneEvents (hypoxia_filt,基因=“STAT2”,罗斯福= 0.05,deltaPSI = 0.1) plotTranscripts (stat2_events类型=“扶轮”,event_id = 3785, gtf = ens_gtf变焦= FALSE ) ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- il32_events < - geneEvents (hypoxia_filt,基因=“IL32”,罗斯福= 0.05,deltaPSI = 0.1) plotTranscripts (il32_events类型=“得到”,event_id = 1136,gtf = ens_gtf变焦= FALSE ) ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- # 投产事件bcs1l_gene < - geneEvents (hypoxia_filt基因=“BCS1L”,罗斯福= 0.05,deltaPSI = 0.1) plotTranscripts (bcs1l_gene类型=“投产”,event_id = 3988, gtf = ens_gtf变焦= TRUE ) ## ---- 回声= FALSE -------------------------------------------------------------- sessionInfo ()