Package 'SMTrackR'

Title: SMTrackR: an R/Bioconductor package for mapping protein binding at individual DNA molecules
Description: The package uses exogenous enzyme imprinted information to map protein-DNA binding on individual sequenced DNA molecules. For example, GpC methyltransferase, CpG methyltransferase, and Adenine methyltransferases. Public datasets from such assays are compiled into tracks, and hosted at public servers like Galaxy for their seamless access by this package.
Authors: Aashna Bansal [aut, ctb], Himani Barmola [aut, ctb], Shivam Yadav [aut, ctb], Satyanarayan Rao [aut, cre] (ORCID: <https://orcid.org/0000-0001-7678-3505>)
Maintainer: Satyanarayan Rao <[email protected]>
License: MIT + file LICENSE
Version: 1.1.0
Built: 2026-06-04 07:15:27 UTC
Source: https://github.com/bioc/SMTrackR

Help Index

Visualize Single Molecule Footprint Patterns with Ideogram and Gene Tracks

Description

Generates Gviz-compatible R code that puts SMF footprints below ideogram and genetracks. This call assumes that you have already ran 'plotFootprints' function. Designed for Drosophila melanogaster analysis with expandable parameters for other organisms.

Usage

generateGvizCodeforSMF(
  organism = "demlanogaster",
  model = "S2",
  condition = "WT",
  genome_assembly = "dm6",
  type = "dSMF",
  chromosome = "chr2L",
  start = 480290,
  end = 480320,
  tr = "fp_and_mvec",
  label = "peak229",
  span_left = 150,
  span_right = 150,
  remove_dup = FALSE,
  fp_cap = 50,
  gviz_left = 1000,
  gviz_right = 1000,
  target_dir = ""
)

Arguments

organism

Organism code (default: "dmelanogaster")
model

Biological model/system (default: "S2" cells)
condition

Experimental condition (default: "WT")
genome_assembly

Genome version (default: "dm6")
type

Data type ("dSMF" = dual enzyme Single Molecule Footprinting)
chromosome

Chromosome ID (e.g., "chr2L")
start

Genomic start position (numeric/character)
end

Genomic end position (numeric/character)
tr

Track name for BigBed file resource (default: "fp_and_mvec")
label

Plot title annotation
span_left

Upstream window size from region (default: 150)
span_right

Downstream window size from region (default: 150)
remove_dup

Remove duplicate reads? (default: FALSE)
fp_cap

Maximum footprint value for y-axis scaling (default: 50)
gviz_left

left zoom (bases) from the start
gviz_right

right zoom (bases) from the end
target_dir

destination directory (must be the same used in 'plotFootprints' function)

Details

This function generates a R code running which one can get ideogram, genetracks and SMF heatmap altogether in one plot.

Value

Saves a heatmap in pdf, png, and eps file formats.

Examples

# Basic usage with default parameters
generateGvizCodeforSMF(organism = "mmusculus", model = "16cell", 
                         condition = "WT", genome_assembly = "mm10",
                         type = "SMF", chromosome = "chr1",start = 191718250,
                         end = 191718280, tr = "16cell", label = "tss",
                         fp_cap = 50, remove_dup = FALSE, gviz_left = 500,
                         gviz_right = 500, target_dir = "")

Discover Available Single Molecule Data Tracks

Description

Retrieves track metadata from a centralized Google Sheet containing organism-specific single-molecule datasets and experimental conditions.

Usage

listTracks()

Value

A tibble containing track metadata with columns:

  • organism: Species identifier (e.g. "dmelanogaster")

  • genome_assembly: Reference genome version

  • condition: Experimental condition

  • model: Biological model/system

  • track_name: Identifier for 'tr' parameter in 'plotFootprints'

  • data_type: NOME-seq protocol variant

  • bigbed_url: Cloud-hosted data location

See Also

'plotFootprints()': Use track names from this list to visualize specific datasets

Examples

# List all available tracks from default repository
listTracks()

Visualize Single Molecule Footprint Patterns

Description

Generates footprint plots from NOME-seq data within specified genomic regions. Designed for Drosophila melanogaster analysis with expandable parameters for other organisms.

Usage

plotFootprints(
  organism = "dmelanogaster",
  model = "S2",
  condition = "WT",
  genome_assembly = "dm6",
  type = "dSMF",
  chromosome = "chr2L",
  start = 480290,
  end = 480320,
  tr = "fp_and_mvec",
  label = "peak229",
  span_left = 150,
  span_right = 150,
  remove_dup = FALSE,
  fp_cap = 50,
  target_dir = ""
)

Arguments

organism

Organism code (default: "dmelanogaster")
model

Biological model/system (default: "S2" cells)
condition

Experimental condition (default: "WT")
genome_assembly

Genome version (default: "dm6")
type

Data type ("dSMF" = dual enzyme Single Molecule Footprinting)
chromosome

Chromosome ID (e.g., "chr2L")
start

Genomic start position (numeric/character)
end

Genomic end position (numeric/character)
tr

Track name for BigBed file resource (default: "fp_and_mvec")
label

Plot title annotation
span_left

Upstream window size from region (default: 150)
span_right

Downstream window size from region (default: 150)
remove_dup

Remove duplicate reads? (default: FALSE)
fp_cap

Maximum footprint value for y-axis scaling (default: 50)
target_dir

destination directory where outputs will be stored

Details

This function retrieves and visualizes DNA accessibility patterns from single-molecule data: - Integrates with UCSC-style track hubs via 'tr' parameter - Automatically handles coordinate conversion for dm6 genome - Implements dynamic y-axis scaling using 'fp_cap'

Value

Saves a heatmap in pdf, png, and eps file formats. Also, occupancies are saved in a tsv file

Examples

# Basic usage with default parameters
plotFootprints()

# Custom genomic region analysis
plotFootprints(
  chromosome = "chr2L", start = 480290, end = 480320, label = "peak229")

Visualize Single Molecule Footprint Patterns using Local BigBed file

Description

Generates footprint plots from SMF/dSMF data within specified genomic regions. Designed for Drosophila melanogaster analysis with expandable parameters for other organisms.

Usage

plotFootprintsUsingLocalBigBed(
  bigBed = "",
  organism = "dmelanogaster",
  model = "S2",
  condition = "WT",
  genome_assembly = "dm3",
  chromosome = "chr2L",
  start = 480290,
  end = 480320,
  label = "peak229",
  span_left = 150,
  span_right = 150,
  remove_dup = FALSE,
  fp_cap = 50,
  target_dir = ""
)

Arguments

bigBed

BigBed file path (e.g., "demo.bb")
organism

Organism code (default: "dmelanogaster")
model

Biological model/system (default: "S2" cells)
condition

Experimental condition (default: "WT")
genome_assembly

Genome version (default: "dm6")
chromosome

Chromosome ID (e.g., "chr2L")
start

Genomic start position (numeric/character)
end

Genomic end position (numeric/character)
label

Plot title annotation
span_left

Upstream window size from region (default: 150)
span_right

Downstream window size from region (default: 150)
remove_dup

Remove duplicate reads? (default: FALSE)
fp_cap

Maximum footprint value for y-axis scaling (default: 50)
target_dir

destination directory where outputs will be stored

Details

This function uses local SMF/dSMF bigBed file and plot heatmap

Value

Saves a heatmap in pdf, png, and eps file formats. Also, occupancies are saved in a tsv file

Examples

# Basic usage with default parameters
plotFootprintsUsingLocalBigBed()

# Custom genomic region analysis
plotFootprintsUsingLocalBigBed(
  bigBed = "inst/extdata/demo.bb", organism = "dmelanogaster",
  model = "S2", condition = "WT", genome_assembly = "dm3",
  chromosome = "chr2L", start = 480290, end = 480320, label = "peak229")

Visualize Single Molecule Footprint Patterns

Description

Generates footprint plots from NOME-seq data within specified genomic regions. Designed for Drosophila melanogaster analysis with expandable parameters for other organisms.

Usage

plotMethylationCallsNanopore(
  organism = "scerevisiae",
  model = "BY4741 strain",
  condition = "WT",
  genome_assembly = "sacCer3",
  type = "SMF",
  chromosome = "chrIII",
  start = 114300,
  end = 114600,
  tr = "nanopore_meth_calls",
  label = "smac_seq",
  span_left = 1000,
  span_right = 1000,
  stride = 5,
  target_dir = ""
)

Arguments

organism

Organism code (default: "scerevisiae")
model

Biological model/system (default: "BY4741 strain")
condition

Experimental condition (default: "WT")
genome_assembly

Genome version (default: "sacCer3")
type

Data type ("Nanopore" = dual enzyme Single Molecule Footprinting)
chromosome

Chromosome ID (e.g., "chrIII")
start

Genomic start position (numeric/character)
end

Genomic end position (numeric/character)
tr

Track name for BigBed file resource (default: "nanopore_meth_calls")
label

Plot title annotation (default: "smac_seq")
span_left

Upstream window size from region (default: 1000)
span_right

Downstream window size from region (default: 1000)
stride

sliding window used for singal aggregation
target_dir

destination directory where outputs will be stored

Details

This function retrieves and visualizes DNA accessibility patterns from single-molecule data: - Integrates with UCSC-style track hubs via 'tr' parameter - Automatically handles coordinate conversion for dm6 genome - Implements dynamic y-axis scaling using 'fp_cap'

Value

Saves a heatmap in pdf, png, and eps file formats. Also, occupancies are saved in a tsv file

Examples

# Basic usage with default parameters
plotMethylationCallsNanopore()

# Custom genomic region analysis

plotMethylationCallsNanopore (
        organism = "scerevisiae", model = "BY4741 strain",
        condition = "WT", genome_assembly = "sacCer3",
        type = "SMF", chromosome = "chrIII",
        start = 114300, end = 114600,
        tr = "nanopore_meth_calls", label = "smac_seq",
        span_left = 1000, span_right = 1000, stride = 5, target_dir = "")

Visualize aggregate methylation calls from ONT sequencing data

Description

Generates heatmap of methylation calls from likes of SMAC-seq datasets. currently has data from Yeast (sacCer3)

Usage

plotMethylationCallsNanoporeUsingLocalBigBed(
  bigBed = "",
  chromosome = "chrIII",
  start = 114300,
  end = 114600,
  label = "smac_seq",
  span_left = 1000,
  span_right = 1000,
  remove_dup = FALSE,
  stride = 5,
  target_dir = ""
)

Arguments

bigBed

BigBed file path (e.g., "demo.bb")
chromosome

Chromosome ID (e.g., "chr2L")
start

Genomic start position (numeric/character)
end

Genomic end position (numeric/character)
label

Plot title annotation
span_left

Upstream window size from region (default: 150)
span_right

Downstream window size from region (default: 150)
remove_dup

Remove duplicate reads? (default: FALSE)
stride

a window size used for averaging the methylation call values
target_dir

destination directory where outputs will be stored

Details

This function uses local SMF/dSMF bigBed file and plot heatmap

Value

Saves a methylation calls (binary) heatmap in pdf, png, and eps file formats.