trimColData: Minimize the number of variables in colData

In waldronlab/BiocInterfaces: TCGA utility functions for data management

Minimize the number of variables in colData

Description

This function removes variables that have a high number of missing data and contain keywords.

Usage

trimColData(
  multiassayexperiment,
  maxNAfrac = 0.2,
  keystring = c("portion", "analyte")
)

Arguments

multiassayexperiment	A MultiAssayExperiment object with colData
maxNAfrac	(numeric default 0.2) A decimal between 0 and 1 to indicate the amount of NA values allowed per column
keystring	(character) A vector of keywords to match and remove variables

Value

A MultiAssayExperiment object

Examples

example(getSubtypeMap)

(gbm_trimmed <- trimColData(gbm))

head(colData(gbm_trimmed))[1:5]

waldronlab/BiocInterfaces documentation built on Dec. 19, 2024, 2:07 p.m.