Added a synthetic transcript example

tutorial/easyRNASeq/synthetic-transcript-creation-example.R

+#' ---
+#' title: "Synthetic transcripts generation example"
+#' author: "Nicolas Delhomme"
+#' date: "`r Sys.Date()`"
+#' output:
+#'  html_document:
+#'    toc: true
+#'    number_sections: true
+#' ---
+#'
+#' # Setup
+#' Load the libraries
+library(easyRNASeq)
+suppressPackageStartupMessages(library(IRanges))
+suppressPackageStartupMessages(library(genomeIntervals))
+library(pander)
+
+#' Source an helper file
+source("https://microasp.upsc.se/root/upscb-public/raw/master/src/R/createSyntheticTranscripts.R")
+
+#' # Process
+#' ## Synthetic transcripts creation
+#' This function takes a gtf or gff3 _filename_ as input.
+#'
+#' The _input_ parameter defines the file format (default to gff3).
+#'
+#' The _feature_ parameter defines which feature to look for in the provided
+#' file. Commonly mRNA for gff3 and transcript for gtf. It defaults to mRNA.
+#' Several parameter can ge given as argument.
+#'
+#' The _output_ paramter defines the type of object that is returned.
+#' It can generate a **Genome_intervals** or a __GRanges__ class of objects.
+#' The former can be saved as a gff3 using the writeGff3 function from the
+#' genomeIntervals package (loaded). The latter can be saved as an RData object
+#' and/or be used directly in the construction of an AnnotParam.
+gAnnot <- createSyntheticTranscripts(
+  filename="~/Box Sync/Projects/easyRNASeq/Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz",
+  input="gtf",
+  feature="transcript",
+  output="GRanges")
+
+#' ## Export
+#' Save the object for later re-use
+save(gAnnot, file="Drosophila_melanogaster.BDGP5.77-synthetic-transcripts.rda")
+
+#' ## Summarization
+#' ### Set the params
+param <- RnaSeqParam(annotParam=AnnotParam(datasource=gAnnot),
+                     bamParam=BamParam(paired=FALSE))
+
+#' ### Get the BAM files
+bamFiles <- getBamFileList(filenames=
+                             dir(system.file(package="RnaSeqTutorial","extdata"),
+                                 pattern="[A,T].*.bam$",
+                                 full.names=TRUE))
+
+#' ### Run
+sexp <- simpleRNASeq(bamFiles=bamFiles,param=param,verbose=TRUE)
+
+#' ### Check
+pander(colSums(assay(sexp)))
+
+#' # Session Info
+sessionInfo()