Heatmap_kdeg: Creating a L2FC(kdeg) matrix that can be passed to heatmap...

In bakR: Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets

Creating a L2FC(kdeg) matrix that can be passed to heatmap functions

Description

Heatmap_kdeg creates a matrix where each column represents a pair of samples (reference and experimental) and each row represents a feature. The entry in the ith row and jth column is the L2FC(kdeg) for feature i when comparing sample with experimental ID j+1 to the reference sample

Usage

Heatmap_kdeg(obj, zscore = FALSE, filter_sig = FALSE, FDR = 0.05)

Arguments

obj	Object outputted by bakRFit
zscore	Logical; if TRUE, then each matrix entry is log-odds fold change in the fraction new (a.k.a the effect size) divided by the uncertainty in the effect size
filter_sig	Logical; if TRUE, then only features which have a statistically significant L2FC(kdeg) in at least one comparison are kept
FDR	Numeric; False discovery to control at if filter_sig is TRUE.

Value

A matrix. Rows represent transcripts which were differentially expressed and columns represent (from left to right) differential kinetics z-score, differential expression z-score, and a mechanism score where positive represents synthesis driven and negative degradation driven changes in expression.

Examples

# Simulate data
sim <- Simulate_bakRData(1000)

# Fit data with fast implementation
Fit <- bakRFit(sim$bakRData)

# L2FC(kdeg) heatmap matrix
L2FC_kdeg_heat <- Heatmap_kdeg(Fit$Fast_Fit)

bakR documentation built on June 22, 2024, 6:55 p.m.