calculate_first_minimum_density {noisyr}

Function to find the first local minimum of the density of a vector

Description

This function is used to estimate the first local minimum of the density of a vector. It is meant to be used on the distribution of expression of genes in a sample; since the distribution tails off, finding the global minimum is not appropriate. The plot option can be used to visualise the process.

Usage

calculate_first_minimum_density(
  mat,
  log.transform = TRUE,
  adjust = 2,
  makeplots = FALSE
)

Arguments

mat

matrix whose columns will be used; usually an expression matrix; it can also be a vector

log.transform

whether to log-transform the data before the density estimation; default is TRUE

adjust

adjust factor for the smoothing, passed to density(); default is 2

makeplots

a logical value of whether a plot with a vertical line on the minimum found should be printed for each column of the matrix.

Value

The function outputs a single value corresponding to the median of the minima calculated for each column of the matrix. floor() is taken as a conservative estimate

Examples

calculate_first_minimum_density(
  matrix(c(rep(0,100),rep(3,30),rep(10,50),12,13,15,20),ncol=1),
  log.transform=FALSE, makeplots=TRUE
)