Bioconductor Tfbstools

TFBSTools

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.

• Version: 1.50.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Imports: Biobase, Biostrings, pwalign, BiocGenerics, BiocParallel, BSgenome, caTools, DirichletMultinomial, Seqinfo, GenomicRanges, gtools, IRanges, DBI, RSQLite, rtracklayer, seqLogo, S4Vectors, TFMPvalue, XML, XVector
• Install: BiocManager::install("TFBSTools")

When to Use

• Matrix Conversion: Converting Position Frequency Matrices (PFMs) to Position Weight Matrices (PWMs) or Information Content Matrices (ICMs) using toPWM and toICM.
• Motif Scanning: Scanning nucleotide sequences or pairwise alignments for transcription factor binding sites using searchSeq or searchAln.
• Database Querying: Querying and retrieving matrix data from the JASPAR database using getMatrixSet.
• Random Profile Generation: Generating random profile matrices via permutation or Dirichlet multinomial mixture models using permuteMatrix and rPWMDmm.
• Visualization: Visualizing sequence logos for basic PWMs or Transcription Factor Flexible Models (TFFMs) using seqLogo.

When NOT to Use

• For high-throughput scanning of thousands of large genomic regions, use motifmatchr instead, because searchSeq is optimized for targeted DNAString or DNAStringSet objects rather than massive GRanges peak sets.
• For de novo motif discovery without external dependencies, use universalmotif because runMEME requires the external MEME suite to be installed on the system.

Data Requirements

• Input Format: PFMatrix objects, DNAString or DNAStringSet for sequences, and Axt objects for alignments.
• Structure: 4-row matrices representing A, C, G, T counts or probabilities.
• Normalization State: Raw position frequency counts for PFMs, which are then converted to log2 probability ratios for PWMs.

Key Parameters

• type (default): The type of matrix conversion in toPWM (e.g., "log2probratio") or the type of p-value calculation in pvalues (e.g., "TFMPvalue").
• pseudocounts (default): Numeric value (default 0.8) added to correct small counts or eliminate zero values before log transformation in toPWM.
• bg (default): A named numeric vector representing background nucleotide frequencies (e.g., c(A=0.25, C=0.25, G=0.25, T=0.25)).
• min.score (default): Minimum score threshold (e.g., "60%" or "80%") for a sequence match to be reported in searchSeq or searchAln.
• schneider (default): Logical in toICM indicating whether to apply the Schneider correction.
• strand (default): Controls which strand is searched in searchSeq (e.g., "*" for both strands).

Best Practices

• Use pseudocounts=0.8 in toPWM rather than the square root of sequences to avoid overly harsh corrections on zero values.
• When scanning sequences with searchSeq, use pvalues with type="TFMPvalue" to calculate empirical p-values for the match scores.
• Use writeGFF3 or writeGFF2 to export SiteSet objects into standard genomic formats for downstream visualization.

Common Pitfalls

• Pitfall: runMEME fails to execute.
  Fix: Ensure the external MEME software suite is installed and the binary argument correctly points to the executable.
• Pitfall: searchSeq returns too many false positive hits.
  Fix: Increase the min.score threshold (e.g., from "60%" to "90%") to enforce stricter matching.
• Pitfall: toPWM throws an error due to zero counts.
  Fix: Ensure pseudocounts is set to a positive value (like 0.8) to eliminate zero values before log transformation.

Alternatives

• motifmatchr: For faster, parallelized motif scanning across large GRanges objects.
• universalmotif: For comprehensive motif manipulation and de novo discovery without relying strictly on external binaries like MEME.
• Biostrings: For basic PWM matching (matchPWM), though it lacks the advanced statistical models and TFFM support of TFBSTools.

Citations

• Tan G, Lenhard B (2016). TFBSTools: an R/Bioconductor package for transcription factor binding site analysis. Bioinformatics.
• Mathelier and Wasserman (2013). The next generation of transcription factor binding site, TFFM.

References

• Homepage: https://bioconductor.org/packages/TFBSTools
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/TFBSTools/inst/doc/TFBSTools.html

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