ImportDeepSignalModFrequency: ImportDeepSignalModFrequency Function (DaLoad)

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

ImportDeepSignalModFrequency Function (DaLoad)

Description

Import DeepSignal call_modification_frequency.py output file and convert it as an UnStitched GPos object.

Usage

ImportDeepSignalModFrequency(
  cDeepSignalModPath,
  cColumnNames = c("chrom", "pos", "strand", "pos_in_strand", "prob_0_sum",
    "prob_1_sum", "count_modified", "count_unmodified", "coverage",
    "modification_frequency", "k_mer"),
  cSelectColumnsToExtract = c("chrom", "pos", "strand", "prob_0_sum", "prob_1_sum",
    "count_modified", "count_unmodified", "coverage", "modification_frequency", "k_mer"),
  lSortGPos = TRUE,
  cContigToBeAnalyzed,
  lKeepSequence = TRUE
)

Arguments

cDeepSignalModPath	Path to a DeepSignal call_modification_frequency.py output file containing data from all target sites.
cColumnNames	Names for each column in the DeepSignal call_modification_frequency.py output file. Should not be changed unless some columns are missing in the file to be imported. Defaults to c("chrom", "pos", "strand", "pos_in_strand", "prob_0_sum", "prob_1_sum", "count_modified", "count_unmodified", "coverage", "modification_frequency", "k_mer")
cSelectColumnsToExtract	Names of columns to extract from DeepSignal call_modification_frequency.py output file. Less there are columns, faster the file will be loaded. The columns "chrom", "pos" and "strand" are mandatory to convert to a GPos object. Defaults to c("chrom", "pos", "strand", "prob_0_sum", "prob_1_sum", "count_modified", "count_unmodified", "coverage", "modification_frequency", "k_mer")
lSortGPos	If TRUE, the GPos object will be sorted before being returned: the function will take a longer time to proceed but the GPos Object will require less memory.
cContigToBeAnalyzed	Names of contigs for which the data will be kept. If NULL, data from all contigs available will be imported. Defaults to NULL.
lKeepSequence	If TRUE, the sequence of the base will be retained in one column. Otherwise, it will be discarded to reduce object size. Defaults to TRUE.

Examples

# 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"
)
mygposDeepSignalModBase

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