associate_with_tsr: Associate TSSs

In zentnerlab/TSRexploreR: TSS and TSR Analysis

Associate TSSs

Description

Associate TSSs with TSRs.

Usage

associate_with_tsr(experiment, sample_list = NULL)

Arguments

experiment	TSRexploreR object.
sample_list	List with TSRs as names and TSSs as vector. If NULL, will associate TSSs with TSRs from the sample of the same name.

Details

TSRexploreR provides many options for the import and merging of TSSs and TSRs. Because of this, TSS samples must be associated with TSR samples after TSR import, TSR merging, or TSS clustering using this function. Each TSS with genomic coordinates overlapping those of a TSR in the specified sample will be linked to that TSR. TSSs not overlapping a TSR in the specified sample will not be associated with any TSR.

TSS samples can be associated with TSR samples using a list or sample sheet. 'sample_list' should be a named list of character vectors, with the names being the TSR sample names and the character vectors as the TSS samples(s) that should be associated with each TSR sample. If no sample list is provided, the function will automatically associate TSSs with the TSRs from the sample of the same name.

Examples

data(TSSs_reduced)

exp <- TSSs_reduced %>%
  tsr_explorer %>%
  format_counts(data_type="tss") %>%
  tss_clustering(threshold=3) %>%
  associate_with_tsr

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