## ----style, echo=FALSE, results='asis'---------------------------------------- BiocStyle::markdown() ## ----echo=FALSE, results="hide", warning=FALSE-------------------------------- suppressPackageStartupMessages({library('fcScan')}) ## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----echo=FALSE, results='asis'----------------------------------------------- df <- data.frame(seqnames = c("chr1", "chr1", "chr1", "chr1", "chr1", "chr1"), start = c(10, 17, 25, 27, 32, 41), end = c(15, 20, 30, 35, 40, 48), strand = c("+", "+", "+", "+", "+", "+"), site = c("a", "b", "b", "a", "c", "b")) knitr::kable(df) ## ----eval=TRUE---------------------------------------------------------------- x1 = data.frame(seqnames = rep("chr1", times = 17), start = c(1,10,17,25,27,32,41,47,60,70,87,94,99,107,113,121,132), end = c(8,15,20,30,35,40,48,55,68,75,93,100,105,113,120,130,135), strand = c("+","+","+","+","+","+","+","+","+", "+","+","+","+","+","+","+","-"), site = c("s3","s1","s2","s2","s1","s2","s1","s1","s2","s1","s2", "s2","s1","s2","s1","s1","s2")) clusters = getCluster(x1, w = 20, c = c("s1" = 1, "s2" = 1, "s3" = 0), greedy = TRUE, order = c("s1","s2"), site_orientation=c("+","+"), site_overlap = 2, verbose = TRUE) clusters ## ----eval=TRUE---------------------------------------------------------------- suppressMessages(library(GenomicRanges)) x = GRanges( seqnames = Rle("chr1", 16), ranges = IRanges(start = c(10L,17L,25L,27L,32L,41L,47L, 60L,70L,87L,94L,99L,107L,113L,121L,132L), end = c(15L,20L,30L,35L,40L,48L,55L,68L,75L,93L,100L,105L, 113L,120L,130L,135L)), strand = Rle("+",16), site = c("s1","s2","s2","s1","s2","s1","s1","s2", "s1","s2","s2","s1","s2","s1","s1","s2")) clusters = getCluster(x, w = 25, c = c("s1"=1,"s2"=2), s = "+") clusters ## ----------------------------------------------------------------------------- sessionInfo()