reformatFragmentFiles: Reformat Fragment Files to be Tabix and Chr Sorted
In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

reformatFragmentFiles

R Documentation

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.