TSanalysis: Transcript start site (TSS) and end site (TES) analysis

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

Transcript start site (TSS) and end site (TES) analysis

Description

Transcript start site (TSS) and end site (TES) analysis

Usage

TSanalysis(
  data_dir,
  cut_off = 0.05,
  cut_at = "fdr",
  TSS_region = 50,
  TES_region = 50,
  min_read = 2,
  bin = 5
)

Arguments

data_dir	The data directory of TAMA output.
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).
TSS_region, TES_region	An integer of enriched TSS/TES wobbling region. TSSs/TESs locate within enriched site+/-site_region are all treated as high confident sites. Default: 50.
min_read	The minimum reads in the window around TSS/TES to support high confident sites. Default: 2.
bin	An integer of window size to aggregate the reads upstream and downstream a TSS/TES. The total reads in [site-bin,site+bin] will be calculated. Default: 5.

Value

Results are saved in data_di

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