Plot Pooled Plasma and Biological Sample Missing Rates

Description

Calculates the missing rate of the pooled plasma columns and biological sample columns for each metabolite. Plots a scatterplot showing the correspondence between the two.

Usage

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plot_pp_sample_missing(df, ppkey = "PPP", sidkey = "X")

Arguments

df

The metabolomics dataset, ideally read from the read.met function. Each column represents a sample and each row represents a metabolite. Columns should be labeled with some unique prefix denoting whether the column is from a biological sample or pooled plasma sample. For example, all pooled plasma samples may have columns identified by the prefix “PPP” and all biological samples may have columns identified by the prefix “X”. Missing data must be coded as NA. Columns must be ordered by injection order.

ppkey

The unique prefix of pooled plasma samples. Default is "PPP".

sidkey

The unique prefix of biological samples. Default is "X".

Value

Returns a scatterplot comparing the pooled plasma missing rate to the sample missing rate

See Also

See MetProc-package for examples of running the full process.

Examples

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library(MetProc)

#Read in metabolomics data
metdata <- read.met(system.file("extdata/sampledata.csv", package="MetProc"),
headrow=3, metidcol=1, fvalue=8, sep=",", ppkey="PPP", ippkey="BPP")

#Plot the pooled plasma missing rate against the sample missing rate
plot_pp_sample_missing(metdata,ppkey='PPP',sidkey='X')