ComputeSummaryStatistics {grandR}

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