compute_zscore: Computes the thresholded Z score Plots the Z score using...

In mdp: Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls

Description

Computes the thresholded Z score Plots the Z score using control samples to compute the average and standard deviation

Usage

compute_zscore(data, control_samples, measure = c("mean", "median"),
  std = 2)

Arguments

data	Gene expression data with gene symbols in rows, sample names in columns
control_samples	Character vector specifying the control sample names
measure	Either 'mean' or 'median'. 'mean' uses mean and standard deviation. 'median' uses the median and the median absolute deviation to estimate the standard devation (modified z-score).
std	Set as default to 2. This controls the standard deviation threshold for the Z-score calculation. #' Normalised expression values less than 'std' will be set to 0.

Value

zscore data frame

Examples

control_samples <- example_pheno$Sample[example_pheno$Class == 'baseline']
compute_zscore(example_data, control_samples,'median',2)

mdp documentation built on Nov. 8, 2020, 7:51 p.m.