## ----style, echo=FALSE, results='asis'---------------------------------------- BiocStyle::markdown() ## ----BiocManager, eval=FALSE-------------------------------------------------- # if (!require("BiocManager")) # install.packages("BiocManager") # BiocManager::install("cliProfiler") ## ----initialize, results="hide", warning=FALSE, message=FALSE----------------- library(cliProfiler) ## ----------------------------------------------------------------------------- testpath <- system.file("extdata", package = "cliProfiler") ## loading the test GRanges object test <- readRDS(file.path(testpath, "test.rds")) ## Show an example of GRanges object test ## ----------------------------------------------------------------------------- ## the path for the test gff3 file test_gff3 <- file.path(testpath, "annotation_test.gff3") ## the gff3 file can be loaded by import.gff3 function in rtracklayer package shown_gff3 <- rtracklayer::import.gff3(test_gff3) ## show the test gff3 file shown_gff3 ## ----------------------------------------------------------------------------- meta <- metaGeneProfile(object = test, annotation = test_gff3) meta[[1]] ## ----------------------------------------------------------------------------- library(ggplot2) ## For example if user want to have a new name for the plot meta[[2]] + ggtitle("Meta Profile 2") ## ----------------------------------------------------------------------------- meta <- metaGeneProfile(object = test, annotation = test_gff3, include_intron = TRUE) meta[[2]] ## ----------------------------------------------------------------------------- test$Treat <- c(rep("Treatment 1",50), rep("Treatment 2", 50)) meta <- metaGeneProfile(object = test, annotation = test_gff3, group = "Treat") meta[[2]] ## ----eval=FALSE--------------------------------------------------------------- # metaGeneProfile(object = test, annotation = test_gff3, exlevel = 3, # extranscript_support_level = c(4,5,6)) ## ----------------------------------------------------------------------------- meta <- metaGeneProfile(object = test, annotation = test_gff3, split = TRUE) meta[[2]] ## ----------------------------------------------------------------------------- intron <- intronProfile(test, test_gff3) ## ----------------------------------------------------------------------------- intron[[1]] ## ----------------------------------------------------------------------------- intron[[2]] ## ----------------------------------------------------------------------------- intron <- intronProfile(test, test_gff3, group = "Treat") intron[[2]] ## ----------------------------------------------------------------------------- intronProfile(test, test_gff3, group = "Treat", exlevel = 3, extranscript_support_level = c(4,5,6)) ## ----------------------------------------------------------------------------- intronProfile(test, test_gff3, group = "Treat", maxLength = 10000, minLength = 50) ## ----------------------------------------------------------------------------- ## Quick use exon <- exonProfile(test, test_gff3) exon[[1]] ## ----------------------------------------------------------------------------- exon[[2]] ## ----results='hide', warning=FALSE, message=FALSE----------------------------- library(rtracklayer) ## Extract all the exon annotation test_anno <- rtracklayer::import.gff3(test_gff3) test_anno <- test_anno[test_anno$type == "exon"] ## Run the windowProfile window_profile <- windowProfile(test, test_anno) ## ----------------------------------------------------------------------------- window_profile[[1]] ## ----------------------------------------------------------------------------- window_profile[[2]] ## ----------------------------------------------------------------------------- ## Example for running the motifProfile ## The working species is mouse with mm10 annotation. ## Therefore the package 'BSgenome.Mmusculus.UCSC.mm10' need to be installed in ## advance. motif <- motifProfile(test, motif = "DRACH", genome = "BSgenome.Mmusculus.UCSC.mm10", fraction = TRUE, title = "Motif Profile", flanking = 10) ## ----------------------------------------------------------------------------- motif[[1]] ## ----------------------------------------------------------------------------- motif[[2]] ## ----------------------------------------------------------------------------- ## Quick use of geneTypeProfile geneTP <- geneTypeProfile(test, test_gff3) ## ----------------------------------------------------------------------------- geneTP[[1]] ## ----------------------------------------------------------------------------- geneTP[[2]] ## ----------------------------------------------------------------------------- SSprofile <- spliceSiteProfile(test, test_gff3, flanking=200, bin=40) ## ----------------------------------------------------------------------------- SSprofile[[1]] ## ----------------------------------------------------------------------------- SSprofile[[2]] ## ----eval=FALSE--------------------------------------------------------------- # spliceSiteProfile(test, test_gff3, flanking=200, bin=40, exlevel=3, # extranscript_support_level = 6, # title = "Splice Site Profile") ## ----------------------------------------------------------------------------- sessionInfo()