flag_contaminants: Flag contaminants

In antonvsdata/notame: Workflow for non-targeted LC-MS metabolic profiling

Flag contaminants

Description

Flags contaminant features by comparing the median values of blanks and biological samples. Biological sampels are defined as samples that are not marked as blanks and are not QCs. If the median of blanks > the median of biological samples times a set ratio, the feature is flagged as contaminant

Usage

flag_contaminants(
  object,
  blank_col,
  blank_label,
  flag_thresh = 0.05,
  flag_label = "Contaminant"
)

Arguments

object	a MetaboSet object
blank_col	character, the column name in pData with blank labels
blank_label	character, the label for blank samples in blank_col
flag_thresh	numeric, the ratio threshold for flagging contaminants. If the median of blanks > flag_thresh * median of biological samples, the feature gets flagged.
flag_label	character, the label used when flagging contaminants. Can be changed if sample processing contaminants and carryover contaminants are flagged separately.

antonvsdata/notame documentation built on Sept. 14, 2024, 11:09 p.m.