reformatFragmentFiles: Reformat Fragment Files to be Tabix and Chr Sorted

In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

Reformat Fragment Files to be Tabix and Chr Sorted

Description

This function provides help in reformatting Fragment Files for reading in createArrowFiles. It will handle weird anomalies found that cause errors in reading tabix bgzip'd fragment files.

Usage

reformatFragmentFiles(
  fragmentFiles = NULL,
  checkChrPrefix = getArchRChrPrefix()
)

Arguments

fragmentFiles	A character vector the paths to fragment files to be reformatted
checkChrPrefix	A boolean value that determines whether seqnames should be checked to contain "chr". IF set to TRUE, any seqnames that do not contain "chr" will be removed from the fragment files.

Examples

# Get Test Fragments
fragments <- getTestFragments()

# Get Peak Annotations
fragments2 <- reformatFragmentFiles(fragments)

GreenleafLab/ArchR documentation built on Feb. 21, 2025, 3:05 p.m.