methylTFRAnnotationHg38

methylTFRAnnotationHg38 provides the genome annotations methylTFR needs to compute bias-corrected transcription factor deviation scores on hg38.

The package supplies three main resources:

• Binding sites: One GRanges object per motif, with each range extended so that methylation can be read across the footprint window.
• Motif GC frequency tables: Tables recording how each motif's binding sites distribute across genome-wide GC quintiles.
• Genome-wide GC distribution: Data that assigns each methylation call to a GC bin.

Because the data are too large to ship inside the package, they are hosted on AnnotationHub. The data are downloaded dynamically on first use, and subsequent calls are served seamlessly from the local AnnotationHub cache.

Installation

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install(c("AnnotationHub","GenomicRanges", "methylTFRAnnotationHg38"))

Usage

You do not need to interact with AnnotationHub directly; the package's accessors handle resolution automatically. The retrieved objects are passed directly to methylTFR::run_methyltfr().

library(methylTFRAnnotationHg38)

tf_bindsites <- getTFbindsites("altius")
gcfreqs      <- getGCfreq("altius")
gc_dist      <- getGenomeGC()

Available Motif Sets

The currently supported motif sets are: altius, cisbpv2, jaspar2020, and jaspar2020_distal.

Sets ending in _distal provide GC frequency tables computed over distal regulatory regions only. They share unrestricted binding sites with their base set. When using a distal set, pass the base set name to getTFbindsites() and the _distal name to getGCfreq().

Local Directory Usage

By default, the accessors will query AnnotationHub for the required files. However, if you have downloaded the .rds files manually or need to run tests in an environment without internet access, you can bypass the hub.

To read resources from a local directory instead of AnnotationHub, configure the local path using either an R option or an environment variable:

• Option: options(methylTFRAnnotationHg38.datadir = "/path/to/data")
• Environment Variable: Sys.setenv(METHYL_TFRANNOTATION_HG38_DIR = "/path/to/data")