compute_zscore {mdp}R Documentation

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

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)

[Package mdp version 1.10.0 Index]