MACSr

Workflows

Standard Workflow

library(MACSr)

# Call narrow peaks
cp1 <- callpeak(CHIP, CTRL, gsize = 5.2e7, store_bdg = TRUE,
                name = "run_callpeak_narrow0", outdir = tempdir(),
                cutoff_analysis = TRUE)

# Call broad peaks
cp2 <- callpeak(CHIP, CTRL, gsize = 5.2e7, store_bdg = TRUE,
                name = "run_callpeak_broad", outdir = tempdir(),
                broad = TRUE)

Input: ChIP-seq treatment and control alignment files (e.g., BED or BAM format). Output: A macsList object containing paths to called peaks (narrow or broad), summits, and bedGraph files.

When to Use

• Calling narrow or broad peaks from ChIP-seq alignment files using callpeak().
• Performing ATAC-seq chromatin accessibility peak calling using the Hidden Markov Model-based hmmratac().
• Comparing two signal tracks in bedGraph format using bdgcmp() or detecting differential peaks using bdgdiff().
• Predicting fragment size or d from alignment results using predictd().

When NOT to Use

• For initial sequence alignment or quality control of raw fastq files, use aligners like Rsubread or external tools like Bowtie2.
• For downstream peak annotation and motif discovery, use packages like ChIPseeker or motifStack.

Data Requirements

• Alignment files in BED, BAM, or other supported formats (can be gzipped).
• Effective genome size (gsize) corresponding to the organism of interest.