omu (version 1.1.2)

check_zeros: Check data for zeros across samples within factor levels. Will determine if there are more zeros than a user specified threshold within any given factor level(s). Returns a vector of Metabolites that are 0 above the threshold in any given factor level.

Description

Check data for zeros across samples within factor levels. Will determine if there are more zeros than a user specified threshold within any given factor level(s). Returns a vector of Metabolites that are 0 above the threshold in any given factor level.

Usage

check_zeros(
  count_data,
  metadata,
  numerator = NULL,
  denominator = NULL,
  threshold = 25,
  response_variable = "Metabolite",
  Factor
)

Arguments

count_data

A metabolomics count data frame

metadata

Metadata dataframe for the metabolomics count data frame

numerator

String of the first independent variable you wish to test. Defualt is NULL

denominator

String of the second independent variable you wish to test. Default is NULL.

threshold

Integer. A percentage threshold for the number of zeros in a Metabolite. Default is 25.

response_variable

String of the column header for the response variables, usually "Metabolite"

Factor

A factor with levels to test for zeros.

Examples

check_zeros(count_data = c57_nos2KO_mouse_countDF, metadata = c57_nos2KO_mouse_metadata,
Factor = "Treatment")
c57_nos2KO_mouse_countDF[1,3:31] <- 0
check_zeros(count_data = c57_nos2KO_mouse_countDF, metadata = c57_nos2KO_mouse_metadata,
Factor = "Treatment",numerator = "Strep", denominator = "Mock", threshold = 10)