## ----eval=FALSE------------------------------------------------------------ # NL42_100K <- NestLink:::.getReadsFromFastq("inst/extdata/NL42_100K.fastq.gz") # save(NL42_100K, file="inst/extdata/NestLink_NL42_100K.RData") ## ----eval=FALSE------------------------------------------------------------ # # expFile <- query(eh, c("NestLink", "NL42_100K.fastq.gz"))[[1]] # expect_true(file.exists(expFile)) # scratchFolder <- tempdir() # setwd(scratchFolder) # # knownNB_File <- query(eh, c("NestLink", "knownNB.txt"))[[1]] # knownNB_data <- read.table(knownNB_File, # sep='\t', # header = TRUE, # row.names = 1, # stringsAsFactors = FALSE) # # knownNB <- Biostrings::translate(DNAStringSet(knownNB_data$Sequence)) # names(knownNB) <- rownames(knownNB_data) # knownNB <- sapply(knownNB, toString) # # param <- list() # param[['NB_Linker1']] <- "GGCCggcggGGCC" # param[['NB_Linker2']] <- "GCAGGAGGA" # param[['ProteaseSite']] <- "TTAGTCCCAAGA" # param[['FC_Linker']] <- "GGCCaaggaggcCGG" # param[['knownNB']] <- knownNB # param[['nReads']] <- 100 # param[['minRelBestHitFreq']] <- 0.8 # param[['minConsensusScore']] <- 0.9 # param[['maxMismatch']] <- 1 # param[['minNanobodyLength']] <- 348 # param[['minFlycodeLength']] <- 33 # param[['FCminFreq']] <- 1 # # nanobodyFlycodeLinkage.RData <- runNGSAnalysis(file = expFile[1], param) ## ---- echo=TRUE, message=FALSE, warning=FALSE------------------------------ library(NestLink) NB <- getNB() FC <- getFC() ## ---- echo=FALSE, message=FALSE, warning=FALSE----------------------------- library(knitr) kable(head(NB)) kable(head(FC)) ## ----eval=FALSE------------------------------------------------------------ # load("~/Downloads/444589.RData") # library(protViz) # library(NestLink) # WU160118 <- do.call('rbind', lapply(list("F255737", "F255744", "F255747", # "F255749", "F255751", "F255760", "F255761", "F255762"), # function(datfilename){ # df <- as.data.frame.mascot(get(datfilename)) # df$datfilename <- datfilename # df # } # )) # save(WU160118, file = "../inst/extdata/WU160118.RData", # compress = TRUE, compression_level = 9) ## ----echo=TRUE, message=FALSE, warning=FALSE------------------------------- library(ExperimentHub) eh <- ExperimentHub(); load(query(eh, c("NestLink", "WU160118.RData"))[[1]]) class(WU160118) PATTERN <- "^GS[ASTNQDEFVLYWGP]{7}(WR|WLTVR|WQEGGR|WLR|WQSR)$" idx <- grepl(PATTERN, WU160118$pep_seq) WU <- WU160118[idx & WU160118$pep_score > 25,] ## ----echo=FALSE, message=FALSE, warning=FALSE------------------------------ kable(unique(unlist(lapply(strsplit(x=as.character(WU$pep_scan_title), split=";"), function(x)gsub("File:", "", gsub("\\\\", "/", x[1])))))) ## ----eval=TRUE------------------------------------------------------------- fl <- system.file("extdata", "metadata.csv", package='NestLink') kable(metadata <- read.csv(fl, stringsAsFactors=FALSE)) ## ----echo=TRUE, message=FALSE, warning=FALSE, eval=TRUE-------------------- library(ExperimentHub) eh <- ExperimentHub(); query(eh, "NestLink") load(query(eh, c("NestLink", "F255744.RData"))[[1]]) dim(F255744) load(query(eh, c("NestLink", "WU160118.RData"))[[1]]) dim(WU160118) ## ----sessionInfo, echo=FALSE----------------------------------------------- sessionInfo()