GetModReportDeepSignal: GetModReportDeepSignal Function (GloModAn)

In AlexisHardy/DNAModAnnot: Toolbox for DNA Modifications filtering and annotation

GetModReportDeepSignal Function (GloModAn)

Description

Return a report with global characteristics of DNA modifications (Mod) distribution in the genome assembly provided. (adapted to data from DeepSignal software)

Usage

GetModReportDeepSignal(
  dnastringsetGenome,
  grangesGenome,
  gposDeepSignalMod,
  gposDeepSignalModBase,
  cOrgAssemblyName,
  cBaseLetterForMod,
  cModNameInOutput
)

Arguments

dnastringsetGenome	A DNAStringSet object containing the sequence for each contig.
grangesGenome	A GRanges object containing the width of each contig.
gposDeepSignalMod	An UnStitched GPos object containing DeepSignal modified sites data.
gposDeepSignalModBase	An UnStitched GPos object containing DeepSignal modification target sites data.
cOrgAssemblyName	The name of the genome assembly provided.
cBaseLetterForMod	The name of the base letter of the modified base.
cModNameInOutput	Name for the modification in the output.

Examples

# preparing genome (simulated)
myGenome <- Biostrings::DNAStringSet(paste0(rep("ATCG", 100000), collapse = ""))
names(myGenome) <- "NC_000001.11"
myGrangesGenome <- GetGenomeGRanges(myGenome)

# Loading Nanopore data
myDeepSignalModPath <- system.file(
  package = "DNAModAnnot", "extdata",
  "FAB39088-288418386-Chr1.CpG.call_mods.frequency.tsv"
)
mygposDeepSignalModBase <- ImportDeepSignalModFrequency(
  cDeepSignalModPath = myDeepSignalModPath,
  lSortGPos = TRUE,
  cContigToBeAnalyzed = "all"
)

# Filtering
mygposDeepSignalMod <- FiltDeepSignal(
  gposDeepSignalModBase = mygposDeepSignalModBase,
  cParamNameForFilter = "frac",
  nFiltParamLoBoundaries = 0,
  nFiltParamUpBoundaries = 1,
  cFiltParamBoundariesToInclude = "upperOnly"
)$Mod

# Mod report
myReport_Mod <- GetModReportDeepSignal(
  dnastringsetGenome = myGenome,
  grangesGenome = myGrangesGenome,
  gposDeepSignalMod = as(mygposDeepSignalMod, "GRanges"),
  gposDeepSignalModBase = as(mygposDeepSignalModBase, "GRanges"),
  cOrgAssemblyName = "Test_function",
  cBaseLetterForMod = "C", cModNameInOutput = "5mC"
)
myReport_Mod

AlexisHardy/DNAModAnnot documentation built on Feb. 27, 2023, 12:03 a.m.