makeGRBs: makeGRBs

In CNEr: CNE Detection and Visualization

Description

Make Genomic Regulatory Blocks (GRBs) boundaries prediction from a set of CNEs.

Usage

  makeGRBs(x, winSize=NULL, genes=NULL, ratio=1,
           background=c("chromosome", "genome"), minCNEs=1L)

Arguments

x	GRangesList object of a set of CNEs to use.
winSize	integer: the smoothing window size for CNE densities in kb. This value depends on the genome size of the reference genome. A larger genome requires bigger window size. For instance, 300kb is the appropriate window size for the human genome. By default, it is determined internally based on the genome size.
genes	NULL or GRanges object: the protein-coding genes ranges.
ratio	numeric(1): the threshold to control the stringency of the GRBs. Higher value, shorter and fewer GRBs, and vice versa.
background	character(1): can be "chromosome" or "genome". When using slice for the CNE density, the background is calculated on a per-chromosome or whole-genome basis.
minCNEs	integer(1): the minimal number of CNEs that a GRB needs to have.

Details

First we calculate the CNE densities from the CNEs. Then we segment the regions according to the values of CNE densities. The regions with CNE densities above the expected CNE densities * ratio are considered as putative GRBs. Putative GRBs that do not encompass any gene are filtered out. Finally, the GRBs that have fewer than minCNEs number of CNEs will be filtered out.

Value

A GRanges object of GRB coordinates is returned. The numbers of CNEs and the coordinates of CNEs within each GRB are returned as a metadata column.

Author(s)

Ge Tan

Examples

  library(TxDb.Drerio.UCSC.danRer10.refGene)
  refGenesDanRer10 <- genes(TxDb.Drerio.UCSC.danRer10.refGene)
  ancoraCNEsFns <- file.path(system.file("extdata", package="CNEr"), 
                             c("cne2wBf_cypCar1_danRer10_100_100",
                               "cne2wBf_cteIde1_danRer10_100_100",
                               "cne2wBf_AstMex102_danRer10_48_50"))
  cneList <- do.call(GRangesList, 
                     lapply(ancoraCNEsFns, readAncora, assembly="danRer10"))
  names(cneList) <- c("Common carp", "Grass carp", "Blind cave fish")
  seqlengths(cneList) <- seqlengths(TxDb.Drerio.UCSC.danRer10.refGene)[
                           names(seqlengths(cneList))]
  makeGRBs(cneList, winSize=200, genes=refGenesDanRer10, ratio=1.2,
           background="genome")
  makeGRBs(cneList, winSize=200, genes=refGenesDanRer10, ratio=1.2,
           background="chromosome", minCNEs=3L)

CNEr documentation built on Nov. 8, 2020, 5:36 p.m.