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Filter proteins by non-missing proportion and/or count

Source: R/filtering.R
filterNA.Rd

Remove proteins with insufficient non-missing values based on a minimum non-missing proportion threshold, a minimum non-missing count threshold, or both.

Usage

filterNA(dataSet, minProp = 0.51, minCount = NULL, by = "cond", saveRm = TRUE)

Arguments

dataSet

A data frame containing the data signals.

minProp

A numeric value (default = 0.51) specifying the minimum non-missing proportion required for a protein to be retained.

minCount

An integer specifying the minimum non-missing count required for a protein to be retained.

by

A character string (default = "cond") specifying how non-missingness is evaluated.

  • "cond": The non-missing proportion and/or count for a protein must meet the specified threshold (minProp and/or minCount) within each condition. Proteins failing in any condition are filtered out.

  • "all": The overall non-missing proportion and/or count across all samples must meet the specified threshold (minProp and/or minCount).

saveRm

A logical value (default = TRUE) specifying whether to save removed data to current working directory.

Value

A filtered data frame.

Details

  • If minProp is provided, proteins are filtered based on the non-missing proportion.

  • If minCount is provided, proteins are filtered based on the non-missing count.

  • If both are provided, both criteria must be satisfied.

  • At least one of minProp and minCount must be specified.