ComputeSummaryStatistics: Compute summary statistics

In grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Compute summary statistics

Description

Summary statistics are computed for all samples (or cells).

Usage

ComputeSummaryStatistics(
  data,
  pairs = Findno4sUPairs(data),
  coldata = FALSE,
  do.bootstrap = FALSE,
  seed = 1337
)

Arguments

data	a grandR object
pairs	a no4sU pairs list as generated by Findno4sUPairs
coldata	if TRUE, add the coldata table
do.bootstrap	if TRUE, also report standard errors of the 4sU dropout estimated via bootstrapping
seed	the seed for the random number generator for bootstrapping

Value

a table of summary statistics including:

• Mean LFC: the mean absolute log2 fold change of each sample vs the corresponding 4sU naive sample

• 4sU dropout: the estimated 4sU dropout percentage

• p.conv: The 4sU incorporation frequency estimated by GRAND-SLAM

• Frction labelled: the global NTR

grandR documentation built on April 4, 2025, 2:27 a.m.