## ---- eval = TRUE, echo=FALSE, results="hide", warning=FALSE------------------ knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) suppressPackageStartupMessages({ library(GenomicRanges) library(ggplot2) library(magrittr) library(periodicDNA) }) BiocParallel::register(setUpBPPARAM(1), default = TRUE) ## ---- eval = TRUE, echo=FALSE, out.width='100%'------------------------------- knitr::include_graphics( "https://raw.githubusercontent.com/js2264/periodicDNA/master/man/figures/periodicityDNA_principle.png" ) ## ---- eval = TRUE------------------------------------------------------------- library(ggplot2) library(magrittr) library(periodicDNA) # data(ce11_TSSs) periodicity_result <- getPeriodicity( ce11_TSSs[['Ubiq.']][1:500], genome = 'BSgenome.Celegans.UCSC.ce11', motif = 'TT', BPPARAM = setUpBPPARAM(1) ) ## ---- eval = TRUE------------------------------------------------------------- head(periodicity_result$PSD) subset(periodicity_result$periodicityMetrics, Period == 10) ## ---- eval = TRUE, fig.width = 9, fig.height = 3.2, out.width='100%'---------- plotPeriodicityResults(periodicity_result) ## ---- eval = TRUE, fig.width = 9, fig.height = 3.2, out.width='100%'---------- periodicity_result <- getPeriodicity( ce11_TSSs[['Ubiq.']][1:500], genome = 'BSgenome.Celegans.UCSC.ce11', motif = 'TT', n_shuffling = 5 ) head(periodicity_result$periodicityMetrics) subset(periodicity_result$periodicityMetrics, Period == 10) plotPeriodicityResults(periodicity_result) ## ---- eval = TRUE------------------------------------------------------------- data(ce11_proms_seqs) periodicity_result <- getPeriodicity( ce11_proms_seqs, motif = 'TT', BPPARAM = setUpBPPARAM(1) ) subset(periodicity_result$periodicityMetrics, Period == 10) ## ---- eval = FALSE------------------------------------------------------------ # WW_10bp_track <- getPeriodicityTrack( # genome = 'BSgenome.Celegans.UCSC.ce11', # granges = ce11_proms, # motif = 'WW', # period = 10, # BPPARAM = setUpBPPARAM(1), # bw_file = 'WW-10-bp-periodicity_over-proms.bw' # ) ## ---- eval = FALSE, results="hide", warning=FALSE----------------------------- # data(ce11_TSSs) # plotAggregateCoverage( # WW_10bp_track, # ce11_TSSs, # xlab = 'Distance from TSS', # ylab = '10-bp periodicity strength (forward proms.)' # ) ## ---- eval = TRUE, echo=FALSE, out.width='100%'------------------------------- knitr::include_graphics( "https://raw.githubusercontent.com/js2264/periodicDNA/master/man/figures/TT-10bp-periodicity_tissue-spe-TSSs.png" ) ## ---- eval = TRUE------------------------------------------------------------- sessionInfo()