Blank filter data by batch

This function will set filtered values to NA. To get a table of the blank values that get dropped use GetBlankDropTable() instead, and then dropBlankFiltered to do the filtering.

Usage

FilterBlanks(inputData, blankFoldThreshold = 5, blankPattern = "PB|blank")

Arguments

inputData

Input metabolite data from ReadFile()

blankFoldThreshold

Fold change threshold below which data are considered blanks

blankPattern

Sample name pattern to use to capture blank. Will match case-insensitively on substring using data.table::like (%ilike)

Value

inputData without the metabolites that don't meet the threshold and without the blanks used for filtering

Details

Adapted from the proteomics blank_filter_by_batch() in "Updated Blank Filter.R". For each metabolite, a sample value must exceed the loudest process blank in its own batch by at least blankFoldThreshold fold; values that don't are set to NA. The blanks are only used to decide what to drop – surviving values keep their original intensities, they are not blank-subtracted. Expects TheData metabolite columns to already be log2 transformed (as they are by the time QCData runs), which makes the fold change a simple subtraction.