total.peak.area: estimates total peak abundance

In MRCIEU/metaboprep: Metabolomics data preparation and processing pipeline

estimates total peak abundance

Description

This function estimates total peak abundance|area for numeric data in a matrix, for (1) all features and (2) all features with complete data.

Usage

total.peak.area(wdata, feature_names_2_exclude = NA, ztransform = TRUE)

Arguments

wdata	the metabolite data matrix. samples in row, metabolites in columns
feature_names_2_exclude	A vector of feature|metabolite names to exclude from the tree building, independent feature identification process.
ztransform	should the feature data be z-transformed and absolute value minimum, mean shifted prior to summing the feature values. TRUE or FALSE.

Value

a data frame of estimates for (1) total peak abundance and (2) total peak abundance at complete features for each samples

Examples

set.seed(1110)
ex_data = sapply(1:5, function(x){ rnorm(10, 40, 5) })
rownames(ex_data) = paste0("ind", 1:nrow(ex_data))
ex_data[ sample(1:50, 4) ] = NA
tpa_est = total.peak.area(ex_data)

MRCIEU/metaboprep documentation built on Jan. 28, 2023, 7:29 p.m.