Filter proteins by missing value criteria — prot.filter_missing • VisomX

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.