## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----BiocManager, eval=FALSE-------------------------------------------------- # if (!require("BiocManager")) # install.packages("BiocManager") # BiocManager::install("rmspc") ## ----initialize, results="hide", warning=FALSE, message=FALSE----------------- library(rmspc) ## ----------------------------------------------------------------------------- path <- system.file("extdata", package = "rmspc") ## ----------------------------------------------------------------------------- list.files(path) ## ----------------------------------------------------------------------------- input1 <- paste0(path, "/rep1.bed") input2 <- paste0(path, "/rep2.bed") input <- c(input1, input2) input ## ----------------------------------------------------------------------------- results <- mspc( input = input, replicateType = "Technical", stringencyThreshold = 1e-8, weakThreshold = 1e-4, gamma = 1e-8, keep = FALSE,GRanges = TRUE, multipleIntersections = "Lowest", c = 2,alpha = 0.05) ## ----------------------------------------------------------------------------- results$status head(results$GRangesObjects,3) ## ----------------------------------------------------------------------------- results$GRangesObjects$ConsensusPeaks results$GRangesObjects$`rep1/Background` ## ----eval=FALSE--------------------------------------------------------------- # BiocManager::install("GenomicRanges",dependencies = TRUE) # BiocManager::install("rtracklayer",dependencies = TRUE) ## ----message=FALSE,warning=FALSE---------------------------------------------- library(GenomicRanges) library(rtracklayer) ## ----------------------------------------------------------------------------- path <- system.file("extdata", package = "rmspc") input1 <- paste0(path, "/rep1.bed") input2 <- paste0(path, "/rep2.bed") GR1 <- rtracklayer::import(con = input1, format = "bed") GR2 <- rtracklayer::import(con = input2, format = "bed") ## ----------------------------------------------------------------------------- GR1 ## ----------------------------------------------------------------------------- GR <- GenomicRanges::GRangesList("GR1" = GR1, "GR2" = GR2) GR ## ----------------------------------------------------------------------------- results <- mspc( input = GR, replicateType = "Biological", stringencyThreshold = 1e-8, weakThreshold = 1e-4, gamma = 1e-8, GRanges = TRUE, keep = FALSE, multipleIntersections = "Highest", c = 2,alpha = 0.05) ## ----------------------------------------------------------------------------- results$status tail(results$GRangesObjects) ## ----SessionInfo-------------------------------------------------------------- sessionInfo()