tsr_explorer-class: TSRexploreR Class

In zentnerlab/TSRexploreR: TSS and TSR Analysis

TSRexploreR Class

Description

This function generates a new TSRexploreR object for detailed analysis of transcription start sites (TSSs) and TSS clusters, referred to here as transcription start regions (TSRs).

Usage

tsr_explorer(
  TSSs = NA,
  TSRs = NA,
  sample_sheet = NULL,
  genome_annotation = NULL,
  genome_assembly = NULL
)

Arguments

TSSs	Named list of TSS GRanges.
TSRs	Named list of TSR GRanges.
sample_sheet	A sample sheet data.frame or tab delimited file. Must have the columns 'sample_name', 'file_1', and 'file_2'. Additional meta-data columns can be added with sample information such as condition and batch.
genome_annotation	Genome annotation in GTF, GFF3, or TxDb format.
genome_assembly	Genome assembly in FASTA or BSgenome format.

Value

A TSRexploreR object containing TSSs and/or TSRs

Slots

experiment

Named lists containing GRanges of TSSs and/or TSRs.

counts

Named lists of normalized TSSs and/or TSRs.

correlation

Named lists of correlation values for TSS and/or TSR sets.

diff_features

Differential features.

shifting

TSS shifting data.

settings

Storage location for arguments used in various functions.

meta_data

Storage for experiment metadata.

See Also

import_bams to import BAM files. tss_import to import TSSs in various formats. tsr_import to import TSRs in various formats.

Examples

data(TSSs)
exp <- tsr_explorer(TSSs)

zentnerlab/TSRexploreR documentation built on Dec. 30, 2022, 10:27 p.m.