# # - eval = FALSE --------------------------------------------------------------- # NL42_100K < - NestLink::: .getReadsFromFastq(“本月/ extdata / NL42_100K.fastq.gz”)#保存(NL42_100K、文件= "本月/ extdata / NestLink_NL42_100K.RData ") ## ---- eval = FALSE --------------------------------------------------------------- # # expFile < -查询(呃,c(“NestLink”、“NL42_100K.fastq.gz”)[[1]]# expect_true (file.exists (expFile)) # scratchFolder < - tempdir () # setwd (scratchFolder) # # knownNB_File < -查询(呃,c(“NestLink”、“knownNB.txt”)[[1]]# knownNB_data < -阅读。table(knownNB_File， # sep='\t'， # header = TRUE， # row.names = 1， # stringsAsFactors = FALSE) # # knownNB <- Biostrings::translate(DNAStringSet(knownNB_data$Sequence)) # names(knownNB) <- rownames(knownNB_data) # knownNB <- sapply(knownNB，toString) # #参数< -列表()#参数[[' NB_Linker1 ']] < -“GGCCggcggGGCC”#参数[[' NB_Linker2 ']] < -“GCAGGAGGA”#参数[[' ProteaseSite ']] < -“TTAGTCCCAAGA”#参数[[' FC_Linker ']] < -“GGCCaaggaggcCGG”#参数[[' knownNB ']] < - knownNB #参数[[' nReads ']] < - 100 #参数[[' minRelBestHitFreq ']] < - 0.8 #参数[[' minConsensusScore ']] < - 0.9 #参数[[' maxMismatch ']] < - 1 #参数[[' minNanobodyLength ']] < - 348 #参数[[' minFlycodeLength ']] < - 33 #参数[[' FCminFreq ']] < - 1 # # nanobodyFlycodeLinkage。RData < - runNGSAnalysis(文件= expFile[1],参数 ) ## ---- 呼应= TRUE,消息= FALSE,警告= FALSE --------------------------------- 库(NestLink) NB < - getNB FC < - getFC () () ## ---- 呼应= FALSE,消息= FALSE,警告= FALSE -------------------------------- 库(knitr) kable(头(NB)) kable(头(FC )) ## ---- eval = FALSE --------------------------------------------------------------- # 负载(~ /下载/ 444589. rdata) #库(protViz) #库(NestLink) # WU160118 < -做。call('rbind'， lapply(list("F255737"， "F255744"， "F255747"， # "F255749"， "F255751"， "F255760"， "F255761"， "F255762")， # function(datfilename){# df <- as.data.frame.mascot(get(datfilename))) # df$datfilename <- datfilename # df #} #)) # save(WU160118, file = "../inst/extdata/WU160118. "RData”,#压缩= TRUE, compression_level = 9) # #——回声= TRUE,消息= FALSE,警告= FALSE ---------------------------------- 图书馆(ExperimentHub)呃< ExperimentHub ();负载(查询(呃,c(“NestLink”、“WU160118.RData”)[[1]])类(WU160118)模式< -“^ GS [ASTNQDEFVLYWGP] {7} (WR | WLTVR | WQEGGR |王俐人| WQSR) $”idx < - grepl吴(模式,WU160118 pep_seq美元)< - WU160118 [idx & WU160118美元pep_score > 25 ,] ## ---- 呼应= FALSE,消息= FALSE,警告= FALSE --------------------------------- kable(独特(unlist(拉普兰人(strsplit (x = as.character(吴pep_scan_title美元),分=”;“),函数(x) gsub(“文件:”、“gsub ("\\\\", "/",x [1 ])))))) ## ---- eval = TRUE ---------------------------------------------------------------- fl < -系统。file("extdata"， "metadata.csv"， package='NestLink') kable(元数据<- read.csv(fl, stringsAsFactors=FALSE)) ## ----echo=TRUE, message=FALSE, warning=FALSE, eval=TRUE----------------------- library(ExperimentHub) eh <- ExperimentHub();查询(呃,NestLink)负载(查询(呃,c(“NestLink”、“F255744.RData”)[[1]])暗(F255744)负载(查询(呃,c(“NestLink”、“WU160118.RData”)[[1]])暗(WU160118) # #——sessionInfo回声= FALSE -------------------------------------------------- sessionInfo ()