missingness.sum: missingness summary plots

In MRCIEU/metaboprep: Metabolomics data preparation and processing pipeline

missingness summary plots

Description

This function sumarizes sample and feature missingness in tables and in a summary plot.

Usage

missingness.sum(mydata)

Arguments

mydata

metabolite data matrix, with samples in rows and metabolite features in columns.

Value

a list object of length four with (1) a vector of sample missingess,(2) a vector of feature missingness ,(3) a table summarizing missingness ,(4) a list of ggplot2 plots for sample and feature histogram distribution and summary tables

Examples

ex_data = sapply(1:100, function(x){ rnorm(250, 40, 5) })
## define the data set
rownames(ex_data) = paste0("ind", 1:nrow(ex_data))
colnames(ex_data) = paste0("var", 1:ncol(ex_data))
## add in some missingness
ex_data[sample(1:length(ex_data), 500)] = NA
## Estimate missingness and generate plots
ms = missingness.sum(ex_data)
## plots
ggpubr::ggarrange(plotlist = ms$plotsout, ncol = 2, nrow = 2)

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