Identify data that falls under the provided threshold by batch across batches

Identify data that falls under the provided threshold by batch across batches

Usage

GetBlankDropTable(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

named list where dropTable is a data.table with Sample, Metabolite, value, and Batch and blanks are the Sample names corresponding to blank samples. This table does not contain any of the blanks or other control sequences.

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.