quantileTrim: Advanced usage: Quantile trim a matrix or matrix pair

In MalteThodberg/TeMPO: Tidy Meta Profiles using Bioconductor and the Tidyverse

Description

Internal function for performing the quantile trimming. Removes outlier rows with the highest or lowest sums. If two matrices are supplied, trims both matrices simultaniously.

Usage

quantileTrim(mat1, mat2 = NULL, lower = 0, upper = 1)

## S4 method for signature 'matrix,NULL_OR_missing'
quantileTrim(mat1, mat2 = NULL,
  lower = 0, upper = 1)

## S4 method for signature 'matrix,matrix'
quantileTrim(mat1, mat2 = NULL, lower = 0,
  upper = 1)

Arguments

mat1	matrix: Sites in rows, positions in columns.
mat2	matrix or NULL: Optional second matrix with the same shape.
lower	numeric: Lower cutoff for trimming (between 0-1).
upper	numeric: Upper cutoff for trimming (between 0-1).

Value

trimmed matrix or list of trimmed matrices

Examples

# Make some random matrices
m1 <- replicate(5, rnorm(10))
m2 <- replicate(5, rnorm(10))

# Trim a single matrix
quantileTrim(mat1=m1, upper=0.75)

# Trim a pair of matrices (e.g. forward/reverse strand)
quantileTrim(mat1=m1, mat2=m2, upper=0.75)

MalteThodberg/TeMPO documentation built on May 15, 2019, 11:48 a.m.