HCsite: Extract high confident transcript start or end site

In wyguo/RTDBox: High resolution Transcriptome using Single Molecule PacBio Iso-seq data

Extract high confident transcript start or end site

Description

Extract high confident transcript start or end site

Usage

HCsite(
  site_stats,
  cut_off = 0.05,
  cut_at = c("fdr", "pval", "prob"),
  site_region = 50,
  min_read = 2,
  type = c("TSS", "TES")
)

Arguments

site_stats	A DataFrame of TSS or TES statistics generated by SummaryTranSite.
cut_off	A numeric value of BH adjsuted p-value (fdr), p-value or probablity cut-off.
cut_at	The cut_off is applied to "fdr" (adjustd p-value), "pval" (p-value) or "prob" (probability).
site_region	An integer of enriched site region. TSSs/TESs locate within enriched site+/-site_region are all treated as high confident sites.
min_read	The minimum reads in a bin to support high confident sites.
type	"TSS" for transcript start site and "TES" for transcript end site.

Value

A DataFrame of enriched TSS or TES sites.

wyguo/RTDBox documentation built on Jan. 31, 2023, 1:19 a.m.