Filter Outlier Samples Based on Protein Counts

This function identifies and removes entire samples that are considered outliers based on the total number of non-missing proteins identified within them.

The method calculates the mean and standard deviation of protein counts across all samples. A sample is flagged as an outlier if its total protein count falls outside the range defined by a specified number of standard deviations (sds) from the mean.

Usage

filter_outlier_samples(object, sds = 3)

# S4 method for class 'SummarizedExperiment,numeric'
filter_outlier_samples(object, sds = 3)

Arguments

object

A SummarizedExperiment object.

sds

The number of standard deviations from the mean protein count to use as the outlier threshold. Defaults to 3.

Value

A SummarizedExperiment object with the outlier samples removed.