ArchRtoSignac

Fix bug -- Check issues #39 #37
cur_pm <- pm[, grepl(paste0('^',cur_sample, "#"), colnames(pm))]
By including the '^' at the start of the regular expression, we're ensuring that only columns whose names start with cur_sample are selected, preventing unintended matches.

ArchRtoSignac

Fix bugs in ArchR2Signac()

ccf523f

ArchRtoSignac

What's Changed

• ArchR2Signac() now can take a list of fragments paths, which made the function easier to use when fragments files are from entirely different directories

seurat_atac <- ArchR2Signac(
  ArchRProject = proj, # an ArchRProject
  refversion = "hg38",
  samples = samples,
  fragments_dir = fragments_dirs,
  pm = pkm,
  fragments_fromcellranger = "YES",
  annotation = annotations
)

• When fragments_fromcellranger = "NO", please set the file extension for the fragments file, fragments_file_extension <- ".fragments.tsv.gz" or any format that you select
• Updates in readme and function descriptions

Contributors

@rootze added a new function and updated the ArchRSignac Package

Full Changelog: https://github.com/swaruplabUCI/ArchRtoSignac/commits/v1.0.2

ArchRtoSignac

What's Changed

• updates in ArchR2Signac functions to read fragments file not only from 10X Genomics, but also other fragments file not organized as cellranger-atac count outputs.
  Please read the tutorial in README.md https://github.com/swaruplabUCI/ArchRtoSignac
  #' fragments_fromcellranger This is an Yes or No selection ("NO" | "N" | "No" or "YES" | "Y" | "Yes")
  #' fragments_file_extension File_Extension for fragments files (typically they should be '.tsv.gz' or '.fragments.tsv.gz')
• updates in R Documentation
• updates in readme and function descriptions

Contributors

@rootze modified the draft code to functions, added new functions, and made the ArchRtoSignac package
@emilymiyoshi made functions more accessible
@smorabit made the draft code

Full Changelog: https://github.com/swaruplabUCI/ArchRtoSignac/commits/v1.0.1