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Filtering NA's post-imputation

Source: R/filterings.R
filterNA.Rd

Remove proteins with NA values.

Usage

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

Arguments

dataSet

The 2d data set of experimental values.

minProp

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

by

A string (default = "cond") specifying how coverage is evaluated.

  • "cond": The non-missing proportion for a protein must be at least minProp within each condition. Proteins failing in any condition are filtered out.

  • "all": The overall non-missing proportion across all samples must be at least minProp.

saveRm

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

Value

A filtered 2d dataframe.

Details

If proteins that do not meet the imputation requirement are removed, a .csv file is created with the removed data.