## ----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()