format_counts: Format Counts

In zentnerlab/TSRexploreR: TSS and TSR Analysis

Format Counts

Description

Format TSS or TSR counts for further analysis.

Usage

format_counts(experiment, data_type = c("tss", "tsr"), samples = "all")

Arguments

experiment	TSRexploreR object.
data_type	Whether to format TSS ('tss') or TSR ('tsr') counts.
samples	A vector of sample names to analyze.

Details

When TSSs or TSRs are first loaded into the TSRexploreR object they are stored as GRanges objects. This function converts these into data.table format and adds a few columns to facilitate downstream analysis.

Value

TSRexploreR object with properly formatted features in data.table format.

Examples

data(TSSs_reduced)

TSSs_reduced %>%
  tsr_explorer %>%
  format_counts(data_type="tss")

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