ceScan-methods {CNEr} | R Documentation

## ceScan function

### 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)

[Package CNEr version 1.20.0 Index]