Calculate the gene complexity of a CTSS dataset.

This function calculates the gene complexity of a given CTSS dataset.

Usage

calcGeneComplexity(
  object,
  txModels,
  step = 1e+06,
  CTSSunexpressed = 1,
  geneunexpressed = 9,
  minCTSSsupport = 2
)

Arguments

object

A RangedSummarizedExperiment resulting from CAGEfightR::quantifyCTSSs().

txModels

A TxDb object containing the gene models.

step

The step size for the subsampling.

CTSSunexpressed

The count threshold for considering a CTSS to be unexpressed.

geneunexpressed

The count threshold for considering a gene to be unexpressed.

minCTSSsupport

The minimum number of samples a CTSS must be expressed in to be considered.

Value

A data frame containing the number of genes (column "numberGenes") for each sample and target (column "totalTags").