prot.filter_missing: Filter proteins by missing value criteria

In NicWir/VisomX: User-Friendly and Comprehensive Analysis and Visualization of Omics Data

Filter proteins by missing value criteria

Description

Filters a SummarizedExperiment proteomics dataset based on three strategies:

• "complete": keep only proteins with no missing values across all samples,

• "condition": keep proteins with at most thr missing values in at least one condition,

• "fraction": keep proteins with at least min fraction of valid values overall.

Usage

prot.filter_missing(
  se,
  type = c("complete", "condition", "fraction", NULL),
  thr = NULL,
  min = NULL
)

Arguments

se	A SummarizedExperiment object containing proteomics data.
type	Character; one of "complete", "condition", or "fraction".
thr	Numeric; maximum allowed missing values per condition (used when type = "condition").
min	Numeric; minimum fraction of valid (non-NA) values required (used when type = "fraction").

Value

A filtered SummarizedExperiment object.

NicWir/VisomX documentation built on July 17, 2025, 12:08 a.m.