tsr_metrics: TSR Metrics

In rpolicastro/tsrexplorer: TSS and TSR Analysis

Description

Calculate various TSR metrics

TSR shape descriptors such as peaked versus broad can enrich for different functional classes of genes. TSRexploreR allows for the calculation of various common TSR shape indicators such as inter-quantile width (IQR), shape index (broad versus peaked), and peak balance. 'iqr_lower' and 'iqr_upper' determine the upper and lower quantile bounds for calculation.

Usage

tsr_metrics(experiment, iqr_lower = 0.1, iqr_upper = 0.9)

Arguments

experiment	TSRexploreR object.
iqr_lower	Lower IQR cutoff value.
iqr_upper	Upper IQR cutoff value.

Value

TSRexplorer object with TSR metrics added to TSSs and TSRs.

Examples

data(TSSs_reduced)

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

rpolicastro/tsrexplorer documentation built on Oct. 17, 2021, 3:02 p.m.