## ----style, echo=FALSE, results='asis'---------------------------------------- BiocStyle::markdown() ## ----message=FALSE,warning=FALSE,results='hide',echo=FALSE-------------------- options(digits=2) ## ----library------------------------------------------------------------------ library(easyRNASeq) ## ----vignetteData, echo=FALSE------------------------------------------------- vDir <- vignetteData() ## ----P trichocarpa annotation, eval=FALSE------------------------------------- # download.file(url=paste0("ftp://ftp.plantgenie.org/Data/PopGenIE/", # "Populus_trichocarpa/v3.0/v10.1/GFF3/", # "Ptrichocarpa_210_v3.0_gene_exons.gff3.gz"), # destfile=,"./Ptrichocarpa_210_v3.0_gene_exons.gff3.gz") ## ----P trichocarpa annotation download, echo=FALSE---------------------------- file.copy(dir(vDir,pattern="*Ptrichocarpa_210_v3.0_gene_exons.gff3.gz",full.names = TRUE), "./Ptrichocarpa_210_v3.0_gene_exons.gff3.gz") ## ----AnnotParam--------------------------------------------------------------- annotParam <- AnnotParam( datasource="./Ptrichocarpa_210_v3.0_gene_exons.gff3.gz") ## ----create synthetic transcripts--------------------------------------------- annotParam <- createSyntheticTranscripts(annotParam,verbose=FALSE) ## ----save the object---------------------------------------------------------- save(annotParam, file="./Ptrichocarpa_210_v3.0_gene_exons_synthetic-transcripts_annotParam.rda") ## ----create synthetic transcripts as gI--------------------------------------- gI <- createSyntheticTranscripts( "./Ptrichocarpa_210_v3.0_gene_exons.gff3.gz", verbose=FALSE) ## ----export the file---------------------------------------------------------- writeGff3(gI, file="./Ptrichocarpa_210_v3.0_gene_exons_synthetic-transcripts.gff3.gz") ## ----bam files, eval=FALSE---------------------------------------------------- # download.file(url=paste0("ftp://ftp.plantgenie.org/Tutorials/RnaSeqTutorial/", # "data/star/md5.txt"), # destfile="md5.txt") ## ----data, eval=FALSE--------------------------------------------------------- # data(RobinsonDelhomme2014) # lapply(RobinsonDelhomme2014[1:6,"Filename"],function(f){ # # BAM files # download.file(url=paste0("ftp://ftp.plantgenie.org/Tutorials/", # "RnaSeqTutorial/data/star/",f), # destfile=as.character(f)) # # BAM index files # download.file(url=paste0("ftp://ftp.plantgenie.org/Tutorials/", # "RnaSeqTutorial/data/star/",f,".bai"), # destfile=as.character(paste0(f,".bai"))) # }) ## ----data unit test, eval=TRUE, echo=FALSE------------------------------------ # THIS IS A subset of the data (chr 19 only) used to speed up # the vignette creation while still testing capabilities data(RobinsonDelhomme2014) lapply(RobinsonDelhomme2014[1:6,"Filename"],function(f){ # BAM files file.copy( dir(vDir,pattern=paste0(as.character(f),"$"),full.names=TRUE) ,file.path(".",f)) # BAM index files file.copy( dir(vDir,pattern=paste0(as.character(f),".bai"),full.names=TRUE) ,file.path(".",paste0(f,".bai"))) }) ## ----bamParam----------------------------------------------------------------- bamParam <- BamParam(paired = TRUE, stranded = FALSE) ## ----bamFiles----------------------------------------------------------------- bamFiles <- getBamFileList(dir(".","*\\.bam$"), dir(".","*\\.bai$")) ## ----rnaSeqParam-------------------------------------------------------------- rnaSeqParam <- RnaSeqParam(annotParam = annotParam, bamParam = bamParam, countBy = "genes", precision = "read") ## ----simpleRS----------------------------------------------------------------- sexp1 <- simpleRNASeq(bamFiles=bamFiles, param=rnaSeqParam, verbose=TRUE) ## ----cleanup, echo=FALSE------------------------------------------------------ data(RobinsonDelhomme2014) file.remove(c( "./Ptrichocarpa_210_v3.0_gene_exons.gff3.gz", "./Ptrichocarpa_210_v3.0_gene_exons_synthetic-transcripts_annotParam.rda", "./Ptrichocarpa_210_v3.0_gene_exons_synthetic-transcripts.gff3.gz", RobinsonDelhomme2014[1:6,"Filename"], paste0(RobinsonDelhomme2014[1:6,"Filename"],".bai"))) ## ----session info, echo=FALSE------------------------------------------------- sessionInfo()