Determining the peak category (Proximal/Distal/Intragenic). — plotPDI • cisDynet

Determining the peak category (Proximal/Distal/Intragenic).

plotPDI(
  peak_path,
  sample,
  suffix = "_peaks_unique.narrowPeak.bed",
  tss_flank,
  cutoff,
  save_path = NA,
  save_name = NA
)

Arguments

peak_path: The path containing the peak bed files.
sample: Sample names.
suffix: Provide a suffix for the peak file. Default: "_peaks_unique.narrowPeak.bed".
tss_flank: How many bp downstream of the TSS is considered proximal.
cutoff: The distance of peak summit to TSS (bp) to determine the proximal / distal.
save_path: Save file path.
save_name: Save file name.

Examples

plotPDI("F:/CAT/example/peaks/", c("Bulk_B", "Mem_B","Naive_B"),
                  "_peaks_unique.narrowPeak.bed",
                  "F:/CAT/example/hg19_gene_standard.bed", cutoff=3000, tss_flank=1000)
#> Error in checkGeAnno(): Necessary Annotation not exist. Please **addAnnotation** first.