Compute summary statistics — ComputeSummaryStatistics • grandR

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