CNEr (version 1.8.3)

ceScan-methods: ceScan function

Description

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

Usage

ceScan(axts, tFilter, qFilter, qSizes, thresholds="49_50")

Arguments

axts

A Axt object or character object with the paths of axt files.

tFilter

A GRanges object or character object with the path of bed file for target genome filter. This argument can also be missing when target filter is not available.

qFilter

A GRanges object or character object with the path of bed file for query genome filter. This argument can also be missing when query filter is not available.

qSizes

A Seqinfo object which contains the seqnames and seqlengths for query genome. This argument can be missing when qFilter is missing.

thresholds

A character object specifiying the scanning windows and minimal score. It can be specified in th form of "45_50" with scanning windows 50 and minial score 45. More than one thresholds can be provided.

Value

A list of data.frame is returned. Each element of the list is for one threshold.

Methods

signature(axts = "Axt", tFilter = "GRanges", qFilter = "GRanges", qSizes = "Seqinfo")

signature(axts = "Axt", tFilter = "GRanges", qFilter = "missing", qSizes = "missing")

signature(axts = "Axt", tFilter = "missing", qFilter = "GRanges", qSizes = "Seqinfo")

signature(axts = "Axt", tFilter = "missing", qFilter = "missing", qSizes = "missing")

signature(axts = "character", tFilter = "character", qFilter = "character", qSizes = "Seqinfo")

signature(axts = "character", tFilter = "character", qFilter = "missing", qSizes = "missing")

signature(axts = "character", tFilter = "missing", qFilter = "character", qSizes = "Seqinfo")

signature(axts = "character", tFilter = "missing", qFilter = "missing", qSizes = "missing")

Details

ceScan scan the axts alignmnets and identify the CNEs. ceScan can accept axts in Axt object and filter in GRanges object, or directly the axt files and bed files. When the axt files and bed files are ready for computation, it is recommended to use them directly rather than read them into R first. The details of algorithm will given in the vignette.

Examples

  
  axtFilesHg19DanRer7 = file.path(system.file("extdata", package="CNEr"), 
                                  "hg19.danRer7.net.axt")
  axtHg19DanRer7 = readAxt(axtFilesHg19DanRer7)
  axtFilesDanRer7Hg19 = file.path(system.file("extdata", package="CNEr"), 
                                  "danRer7.hg19.net.axt")
  axtDanRer7Hg19 = readAxt(axtFilesDanRer7Hg19)
  bedHg19Fn = file.path(system.file("extdata", package="CNEr"), 
                        "filter_regions.hg19.bed")
  bedHg19 = readBed(bedHg19Fn)
  bedDanRer7Fn = file.path(system.file("extdata", package="CNEr"), 
                           "filter_regions.danRer7.bed")
  bedDanRer7 = readBed(bedDanRer7Fn)
  qSizesHg19 = fetchChromSizes("hg19")
  qSizesDanRer7 = fetchChromSizes("danRer7")
  CNEHg19DanRer7 = ceScan(axts=axtHg19DanRer7, tFilter=bedHg19,
                          qFilter=bedDanRer7, qSizes=qSizesDanRer7,
                          thresholds=c("45_50", "48_50", "49_50"))
  CNEDanRer7Hg19 = ceScan(axts=axtDanRer7Hg19, tFilter=bedDanRer7,
                          qFilter=bedHg19, qSizes=qSizesHg19,
                          thresholds=c("45_50", "48_50", "49_50"))