summarizeMatrix: Summarize matrix

In AllenInstitute/mfishtools: Building Gene Sets and Mapping mFISH Data

Summarize matrix

Description

Groups columns in a matrix by a specified group vector and summarizes using a specificed function. Optionally binarizes the matrix using a specified cutoff parameter. This is a wrapper for tapply.

Usage

summarizeMatrix(
  mat,
  group,
  scale = "none",
  scaleQuantile = 1,
  binarize = FALSE,
  binMin = 0.5,
  summaryFunction = median,
  ...
)

Arguments

mat	matrix where the columns (e.g., samples) are going to be grouped
group	vector of length dim(mat)[2] corresponding to the groups
scale	either 'none' (default),'row', or 'column'
scaleQuantile	what quantile of value should be set as 1 (default=1)
binarize	should the data be binarized? (default=FALSE)
binMin	minimum ON value for the binarized matrix (ignored if binarize=FALSE)
summaryFunction	function (or function name) to be used for summarization
...	additional parameters for summaryFunction

Value

matrix of summarized values

AllenInstitute/mfishtools documentation built on July 5, 2023, 4:20 p.m.