## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ---- eval = FALSE------------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("primirTSS") ## ---- eval = FALSE------------------------------------------------------------ # BiocManager::install("ipumin/primirTSS") ## ----Load, message=FALSE------------------------------------------------------ library(primirTSS) ## ----------------------------------------------------------------------------- library(primirTSS) peak_df <- data.frame(chrom = c("chr1", "chr2", "chr1"), chromStart = c(450, 460, 680), chromEnd = c(470, 480, 710), stringsAsFactors = FALSE) peak <- as(peak_df, "GRanges") peak_merge(peak, n =250) ## ----------------------------------------------------------------------------- peak_df1 <- data.frame(chrom = c("chr1", "chr1", "chr1", "chr2"), start = c(100, 460, 600, 70), end = c(200, 500, 630, 100), stringsAsFactors = FALSE) peak1 <- as(peak_df1, "GRanges") peak_df2 <- data.frame(chrom = c("chr1", "chr1", "chr1", "chr2"), start = c(160, 470, 640, 71), end = c(210, 480, 700, 90), stringsAsFactors = FALSE) peak2 <- as(peak_df2, "GRanges") peak_join(peak1, peak2) ## ----------------------------------------------------------------------------- peakfile <- system.file("testdata", "HMEC_h3.csv", package = "primirTSS") DHSfile <- system.file("testdata", "HMEC_DHS.csv", package = "primirTSS") peak_h3 <- read.csv(peakfile, stringsAsFactors = FALSE) DHS <- read.csv(DHSfile, stringsAsFactors = FALSE) DHS <- as(DHS, "GRanges") peak_h3 <- as(peak_h3, "GRanges") peak <- peak_merge(peak_h3) ## ----------------------------------------------------------------------------- bed_merged <- data.frame( chrom = c("chr1", "chr1", "chr1", "chr1", "chr2"), start = c(9910686, 9942202, 9996940, 10032962, 9830615), end = c(9911113, 9944469, 9998065, 10035458, 9917994), stringsAsFactors = FALSE) bed_merged <- as(bed_merged, "GRanges") expressed_mir <- c("hsa-mir-5697") ownmiRNA <- find_tss(bed_merged, expressed_mir = expressed_mir, ignore_DHS_check = TRUE, expressed_gene = "all", allmirgene_byforce = TRUE, seek_tf = FALSE) ## ----------------------------------------------------------------------------- ownmiRNA$tss_df ## ----------------------------------------------------------------------------- sessionInfo()