## ----message=FALSE------------------------------------------------------- library(psichomics) library(plyr) ## ---- include=FALSE------------------------------------------------------ suppaOutput <- system.file("extdata/eventsAnnotSample/suppa_output/suppaEvents", package="psichomics") suppaFile <- tempfile(fileext=".RDS") ## ------------------------------------------------------------------------ # suppaOutput <- "path/to/SUPPA/output" # Replace `genome` for the string with the identifier before the first # underscore in the filenames of that directory (for instance, if one of your # filenames of interest is "hg19_A3.ioe", the string would be "hg19") suppa <- parseSuppaAnnotation(suppaOutput, genome="hg19") annot <- prepareAnnotationFromEvents(suppa) # suppaFile <- "suppa_hg19_annotation.RDS" saveRDS(annot, file=suppaFile) ## ---- include=FALSE------------------------------------------------------ matsOutput <- system.file("extdata/eventsAnnotSample/mats_output/ASEvents/", package="psichomics") matsFile <- tempfile("mats", fileext=".RDS") ## ------------------------------------------------------------------------ # matsOutput <- "path/to/rMATS/output" mats <- parseMatsAnnotation( matsOutput, # Output directory from rMATS genome = "fromGTF", # Identifier of the filenames novelEvents=TRUE) # Parse novel events? annot <- prepareAnnotationFromEvents(mats) # matsFile <- "mats_hg19_annotation.RDS" saveRDS(annot, file=matsFile) ## ---- include=FALSE------------------------------------------------------ misoAnnotation <- system.file("extdata/eventsAnnotSample/miso_annotation", package="psichomics") misoFile <- tempfile("miso", fileext=".RDS") ## ------------------------------------------------------------------------ # misoAnnotation <- "path/to/MISO/annotation" miso <- parseMisoAnnotation(misoAnnotation) annot <- prepareAnnotationFromEvents(miso) # misoFile <- "miso_AS_annotation_hg19.RDS" saveRDS(annot, file=misoFile) ## ---- include=FALSE------------------------------------------------------ vastAnnotation <- system.file("extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/", package="psichomics") vastFile <- tempfile("vast", fileext=".RDS") ## ------------------------------------------------------------------------ # vastAnnotation <- "path/to/VASTDB/libs/TEMPLATES" vast <- parseVastToolsAnnotation(vastAnnotation, genome="Hsa") annot <- prepareAnnotationFromEvents(vast) # vastFile <- "vast_AS_annotation_hg19.RDS" saveRDS(annot, file=vastFile) ## ---- include=FALSE------------------------------------------------------ annotFile <- tempfile(fileext=".RDS") ## ------------------------------------------------------------------------ # Let's combine the annotation from SUPPA, MISO, rMATS and VAST-TOOLS suppa <- parseSuppaAnnotation(suppaOutput, genome="hg19") miso <- parseMisoAnnotation(misoAnnotation) mats <- parseMatsAnnotation(matsOutput, genome = "fromGTF", novelEvents=TRUE) vast <- parseVastToolsAnnotation(vastAnnotation) annot <- prepareAnnotationFromEvents(suppa, vast, mats, miso) # annotFile <- "AS_annotation_hg19.RDS" saveRDS(annot, file=annotFile) ## ------------------------------------------------------------------------ annot <- readRDS(annotFile) # "file" is the path to the annotation file junctionQuant <- readFile("ex_junctionQuant.RDS") # example set psi <- quantifySplicing(annot, junctionQuant, c("SE", "MXE", "A3SS", "A5SS", "AFE", "ALE")) psi # may have 0 rows because of the small junction quantification set