clean_bmdk: Clean the BMDK data

Description Usage Arguments Value

View source: R/clean_bmdk.R

Description

Identify outliers across samples and across features and set identified values to NA. Features and samples that contain a threshold ratio of NA values are removed.

Usage

1
clean_bmdk(dat, naThreshold = 0.05, sdMultiplier = 4)

Arguments

dat

a list containing 3 elements: case, a list of case/control statuses; feat, a matrix of normalized feature data; maxfeat, a list of max features from each column in feat

naThreshold

Proportion of NAs to allow before dropping a sample or feature due to missingness.

sdMultiplier

Number of standard deviations defining the threshold for outlier detection. Any values above sdMultiplier standard deviations away from the mean will be removed as an outlier.

Value

List containing 3 elements (case, feat, maxfeat) with relevant NA values and necessary features/samples removed


abcsFrederick/BMDK documentation built on Aug. 9, 2021, 2:19 p.m.