ceScan-methods: ceScan function

In CNEr: CNE Detection and Visualization

Description

This is the main function for conserved noncoding elements (CNEs) identification.

Usage

  ceScan(x, tFilter=NULL, qFilter=NULL,
         tSizes=NULL, qSizes=NULL, window=50L, identity=50L)

Arguments

x	CNE object, or Axt object, or character(n) object of Axt filenames.
tFilter,qFilter	GRanges object or NULL: regions to filter out for target and query assembly.
tSizes,qSizes	Seqinfo object or integer(n) or NULL: it contains the seqnames and seqlengths for target and query genome. When it's NULL, this ‘seqinfo’ must exist in ‘x’.
window	integer(n): the window size of scanning CNEs. By default, it is 50L.
identity	integer(n): the minimal identity score over the scanning window. By default, it is 50L.

Details

ceScan scan the axts alignments and identify the CNEs. ceScan can accept axts in Axt object and regions to filter out as GRanges objects, or directly the ‘axt’ files and ‘bed’ files.

The details of the algorithm are described in the vignette.

Value

A list of GRangePairs or CNE object is returned. Each element of the list corresponds to one user-specified threshold for identifying CNEs.

Author(s)

Ge Tan

Examples

  library(BSgenome.Drerio.UCSC.danRer10)
  library(BSgenome.Hsapiens.UCSC.hg38)
  axtFnHg38DanRer10 <- file.path(system.file("extdata", package="CNEr"), 
                                 "hg38.danRer10.net.axt")
  axtHg38DanRer10 <- readAxt(axtFnHg38DanRer10)
  axtFnDanRer10Hg38 <- file.path(system.file("extdata", package="CNEr"), 
                                 "danRer10.hg38.net.axt")
  axtDanRer10Hg38 <- readAxt(axtFnDanRer10Hg38)
  bedHg38Fn <- file.path(system.file("extdata", package="CNEr"), 
                        "filter_regions.hg38.bed")
  bedHg38 <- readBed(bedHg38Fn)
  bedDanRer10Fn <- file.path(system.file("extdata", package="CNEr"), 
                             "filter_regions.danRer10.bed")
  bedDanRer10 <- readBed(bedDanRer10Fn)
  qSizesHg38 <- seqinfo(BSgenome.Hsapiens.UCSC.hg38)
  qSizesDanRer10 <- seqinfo(BSgenome.Drerio.UCSC.danRer10)
  
  ## Axt object
  windows <- c(50L, 50L, 50L)
  identities <- c(45L, 48L, 49L)
  CNEHg38DanRer10 <- ceScan(x=axtHg38DanRer10, tFilter=bedHg38,
                            qFilter=bedDanRer10, 
                            tSizes=qSizesHg38, qSizes=qSizesDanRer10,
                            window=windows, identity=identities)
  CNEDanRer10Hg38 <- ceScan(x=axtDanRer10Hg38, tFilter=bedDanRer10,
                            qFilter=bedHg38, 
                            tSizes=qSizesDanRer10, qSizes=qSizesHg38,
                            window=windows, identity=identities)

  ## CNE object
  cneDanRer10Hg38 <- CNE(
    assembly1Fn=file.path(system.file("extdata",
                                    package="BSgenome.Drerio.UCSC.danRer10"),
                        "single_sequences.2bit"),
    assembly2Fn=file.path(system.file("extdata",
                                    package="BSgenome.Hsapiens.UCSC.hg38"),
                        "single_sequences.2bit"),
    axt12Fn=axtFnDanRer10Hg38, axt21Fn=axtFnHg38DanRer10,
    cutoffs1=8L, cutoffs2=4L)
  ## Here danRer10Filter is tFilter since danRer10 is assembly1
  cneListDanRer10Hg38 <- ceScan(x=cneDanRer10Hg38, tFilter=bedDanRer10,
                                qFilter=bedHg38,
                                window=windows, identity=identities)

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