compute_logratio: Compute activity measure (log-ratio) for each element.

In hansenlab/mpra: Analyze massively parallel reporter assays

Compute activity measure (log-ratio) for each element.

Description

Compute the log ratio of RNA counts to DNA counts using different methods. For "mean", uses the average of barcode-specific log ratios. For "sum", sums RNA and DNA counts over barcodes before forming the log ratio.

Usage

compute_logratio(object, aggregate = c("mean", "sum", "none"))

Arguments

object	An object of class MPRASet.
aggregate	Aggregation method over barcodes: "mean" to use the average of barcode-specific log ratios, "sum" to use the log ratio of summed RNA and DNA counts, "none" to perform no aggregation (counts have already been summarized over barcodes).

Value

A matrix with the same dimension as object, containing element- and sample-specific log ratios.

Examples

  data(mpraSetAggExample)
  logr <- compute_logratio(mpraSetAggExample, aggregate = "sum")

hansenlab/mpra documentation built on Sept. 15, 2024, 4:11 p.m.