Version Compatibility

Reference examples tested with: ggplot2 3.5+, limma 3.58+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Motif Deviation Analysis

"Which TF motifs show variable accessibility across my samples?" → Compute per-sample deviation scores for TF motif accessibility to identify regulators driving chromatin state differences.

• R: chromVAR::computeDeviations(counts, motifs)

Measure per-sample variability in transcription factor motif accessibility using chromVAR. This identifies TFs whose binding sites show differential accessibility across conditions.

Required Packages

library(chromVAR)
library(motifmatchr)
library(BSgenome.Hsapiens.UCSC.hg38)  # or appropriate genome
library(JASPAR2020)
library(TFBSTools)
library(SummarizedExperiment)

Basic Workflow

Goal: Run chromVAR to compute per-sample TF motif deviation scores from ATAC-seq peak counts.

Approach: Load peak counts into a SummarizedExperiment, correct for GC bias, filter low-quality peaks, match JASPAR motifs, and compute deviation z-scores.

1. Load Peak Counts

library(chromVAR)
library(SummarizedExperiment)

# From count matrix and peak ranges
peaks <- read.table('peaks.bed', col.names = c('chr', 'start', 'end'))
peak_ranges <- GRanges(seqnames = peaks$chr, ranges = IRanges(peaks$start, peaks$end))

counts <- read.table('counts.txt', header = TRUE, row.names = 1)
counts_matrix <- as.matrix(counts)

fragment_counts <- SummarizedExperiment(
    assays = list(counts = counts_matrix),
    rowRanges = peak_ranges
)

2. Add GC Bias Correction

library(BSgenome.Hsapiens.UCSC.hg38)

fragment_counts <- addGCBias(fragment_counts, genome = BSgenome.Hsapiens.UCSC.hg38)

3. Filter Low-Quality Peaks

# min_depth=1500: Minimum total reads per sample. Adjust based on library size.
# min_in_peaks=0.15: Minimum fraction of reads in peaks (FRiP). 0.15 = 15%.
fragment_counts <- filterSamples(fragment_counts, min_depth = 1500, min_in_peaks = 0.15)

# min_count=10: Require peaks with >=10 reads across samples.
# n_samples_frac=0.1: Peak must be detected in >=10% of samples.
fragment_counts <- filterPeaks(fragment_counts, non_overlapping = TRUE,
                                min_count = 10, n_samples_frac = 0.1)

Get Motif Annotations

From JASPAR

library(JASPAR2020)
library(TFBSTools)
library(motifmatchr)

# Get vertebrate motifs from JASPAR
pfm <- getMatrixSet(JASPAR2020, opts = list(collection = 'CORE', tax_group = 'vertebrates'))

# Match motifs to peaks
# p.cutoff=5e-5: Motif match p-value threshold. Lower = more stringent.
motif_ix <- matchMotifs(pfm, fragment_counts, genome = BSgenome.Hsapiens.UCSC.hg38, p.cutoff = 5e-5)

From CIS-BP or Custom PWMs

# Load custom motifs from file
library(universalmotif)
motifs <- read_meme('custom_motifs.meme')
pfm_list <- lapply(motifs, function(m) convert_motifs(m, class = 'TFBSTools-PFMatrix'))

motif_ix <- matchMotifs(pfm_list, fragment_counts, genome = BSgenome.Hsapiens.UCSC.hg38)

Compute Deviations

# Compute chromVAR deviation scores
dev <- computeDeviations(object = fragment_counts, annotations = motif_ix)

# Extract deviation scores (z-scores)
deviation_scores <- deviations(dev)

# Extract variability across samples
variability <- computeVariability(dev)

Interpreting Results

Deviation Scores

# Deviation z-scores: positive = more accessible than expected
# Compare across samples
dev_matrix <- deviations(dev)
print(dim(dev_matrix))  # motifs x samples

# Get top variable motifs
var_df <- variability
var_df <- var_df[order(-var_df$variability), ]
head(var_df, 20)

Variability Interpretation

Variability	Interpretation
> 2.0	Highly variable across samples
1.0 - 2.0	Moderately variable
< 1.0	Low variability

Visualization

Deviation Heatmap

library(pheatmap)

# Get top variable motifs
# n_top=50: Number of top variable motifs to display.
n_top <- 50
top_motifs <- head(rownames(var_df), n_top)
top_dev <- deviation_scores[top_motifs, ]

# Add sample annotations
sample_info <- data.frame(
    Condition = colData(fragment_counts)$condition,
    row.names = colnames(top_dev)
)

pheatmap(top_dev, annotation_col = sample_info, scale = 'row',
         clustering_method = 'ward.D2', show_rownames = TRUE)

Variability Plot

plotVariability(variability, use_plotly = FALSE)

PCA of Deviation Scores

library(ggplot2)

# PCA on deviation scores
pca <- prcomp(t(deviation_scores), scale. = TRUE)
pca_df <- data.frame(PC1 = pca$x[,1], PC2 = pca$x[,2],
                     Condition = colData(fragment_counts)$condition)

ggplot(pca_df, aes(x = PC1, y = PC2, color = Condition)) +
    geom_point(size = 3) +
    theme_minimal() +
    labs(title = 'PCA of chromVAR Deviations')

Differential Motif Accessibility

Goal: Identify TF motifs with significantly different accessibility between experimental groups.

Approach: Fit a linear model (limma) to deviation z-scores across groups and extract significant motifs with empirical Bayes moderation.

Compare Two Groups

library(limma)

# Get sample groups
groups <- factor(colData(fragment_counts)$condition)

# Design matrix
design <- model.matrix(~ groups)

# Fit linear model to deviation scores
fit <- lmFit(deviation_scores, design)
fit <- eBayes(fit)

# Get differential motifs
# p.value=0.05: FDR threshold for significance.
diff_motifs <- topTable(fit, coef = 2, number = Inf, p.value = 0.05)
print(head(diff_motifs, 20))

Volcano Plot

library(ggplot2)

all_results <- topTable(fit, coef = 2, number = Inf)
all_results$significant <- all_results$adj.P.Val < 0.05

ggplot(all_results, aes(x = logFC, y = -log10(adj.P.Val), color = significant)) +
    geom_point(alpha = 0.6) +
    geom_hline(yintercept = -log10(0.05), linetype = 'dashed') +
    scale_color_manual(values = c('grey', 'red')) +
    theme_minimal() +
    labs(title = 'Differential Motif Accessibility',
         x = 'Log2 Fold Change', y = '-log10(adjusted p-value)')

Working with Single-Cell ATAC-seq

# For scATAC-seq, aggregate cells by cluster first
# Then run chromVAR on pseudo-bulk profiles

# Or use chromVAR with sparse matrices
library(Matrix)

# Create SummarizedExperiment with sparse counts
sparse_counts <- Matrix(counts_matrix, sparse = TRUE)
fragment_counts <- SummarizedExperiment(
    assays = list(counts = sparse_counts),
    rowRanges = peak_ranges
)

# Proceed with standard workflow
fragment_counts <- addGCBias(fragment_counts, genome = BSgenome.Hsapiens.UCSC.hg38)

Background Peaks Strategy

# Custom background for better bias correction
# n_iterations=50: Number of background sets. Higher = more stable but slower.
bg <- getBackgroundPeaks(object = fragment_counts, niterations = 50)

# Use custom background in deviation calculation
dev <- computeDeviations(object = fragment_counts, annotations = motif_ix, background_peaks = bg)

Export Results

# Save deviation scores
write.csv(as.data.frame(deviation_scores), 'chromvar_deviations.csv')

# Save variability
write.csv(variability, 'chromvar_variability.csv')

# Save differential results
write.csv(diff_motifs, 'differential_motifs.csv')

Complete Workflow

Goal: Run end-to-end chromVAR analysis from peak counts to motif variability scores.

Approach: Load counts, correct GC bias, filter peaks, match JASPAR motifs, compute deviations, and plot variability.

library(chromVAR)
library(motifmatchr)
library(BSgenome.Hsapiens.UCSC.hg38)
library(JASPAR2020)
library(TFBSTools)

# 1. Load data
fragment_counts <- getCounts('peaks.bed', c('sample1.bam', 'sample2.bam', 'sample3.bam'))

# 2. Add GC bias
fragment_counts <- addGCBias(fragment_counts, genome = BSgenome.Hsapiens.UCSC.hg38)

# 3. Filter
fragment_counts <- filterPeaks(fragment_counts)

# 4. Get motifs
pfm <- getMatrixSet(JASPAR2020, opts = list(collection = 'CORE', tax_group = 'vertebrates'))
motif_ix <- matchMotifs(pfm, fragment_counts, genome = BSgenome.Hsapiens.UCSC.hg38)

# 5. Compute deviations
dev <- computeDeviations(fragment_counts, motif_ix)

# 6. Analyze variability
variability <- computeVariability(dev)
plotVariability(variability)

Related Skills

• differential-accessibility - Peak-level differential analysis with DiffBind
• footprinting - TF footprinting with TOBIAS
• atac-qc - Quality control before chromVAR
• chip-seq/motif-analysis - Alternative motif enrichment approaches