MetProc: Separate Metabolites into Likely Measurement Artifacts and True Metabolites
Version 1.0.1

Split an untargeted metabolomics data set into a set of likely true metabolites and a set of likely measurement artifacts. This process involves comparing missing rates of pooled plasma samples and biological samples. The functions assume a fixed injection order of samples where biological samples are randomized and processed between intermittent pooled plasma samples. By comparing patterns of missing data across injection order, metabolites that appear in blocks and are likely artifacts can be separated from metabolites that seem to have random dispersion of missing data. The two main metrics used are: 1. the number of consecutive blocks of samples with present data and 2. the correlation of missing rates between biological samples and flanking pooled plasma samples.

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AuthorMark Chaffin
Date of publication2016-05-19 05:46:39
MaintainerMark Chaffin <mac8278@mail.harvard.edu>
LicenseGPL (>= 2)
Version1.0.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MetProc")

Man pages

corr_metric: Calculate Correlation of Missing Rates between Pooled Plasma...
get_group: Retrieve Index of Biological Samples and Pooled Plasma...
get_missing: Compute Missing Rates of Biological Samples and Pooled Plasma...
heatmap_res: Plot Patterns of Missing Data Across Metabolites
met_proc: Separates Metabolites into Likely True Metabolites and Likely...
MetProc-package: Separate Untargeted Metabolites into Likely Artifacts and...
plot_metric: Plot Distribution of Metabolite Quality Metrics for Each...
plot_pp_sample_missing: Plot Pooled Plasma and Biological Sample Missing Rates
read.met: Read in a Metabolomics Dataset of Standard Structure
run_metric: Calculate Longest Run of Blocks where Data is Present
sampledata: Simulated Metabolomics Data
subset_met: Group Metabolites based on Pooled Plasma Missing Rate
write.met: Write Metabolomics Dataset of Standard Structure

Functions

MetProc Man page
MetProc-package Man page
corr_metric Man page Source code
get_group Man page Source code
get_missing Man page Source code
heatmap_res Man page Source code
met_proc Man page Source code
plot_metric Man page Source code
plot_pp_sample_missing Man page Source code
read.met Man page Source code
run_metric Man page Source code
sampledata Man page
subset_met Man page Source code
write.met Man page Source code

Files

inst
inst/extdata
inst/extdata/sampledata.csv
inst/doc
inst/doc/using-MetProc.html
inst/doc/using-MetProc.R
inst/doc/using-MetProc.Rmd
NAMESPACE
R
R/functions_cleane.R
vignettes
vignettes/using-MetProc.Rmd
vignettes/pp_bio_corr.png
vignettes/removed.png
vignettes/metrics.png
vignettes/retained.png
MD5
build
build/vignette.rds
DESCRIPTION
man
man/sampledata.Rd
man/MetProc-package.Rd
man/subset_met.Rd
man/heatmap_res.Rd
man/run_metric.Rd
man/met_proc.Rd
man/get_missing.Rd
man/plot_pp_sample_missing.Rd
man/write.met.Rd
man/corr_metric.Rd
man/get_group.Rd
man/plot_metric.Rd
man/read.met.Rd
MetProc documentation built on May 19, 2017, 1:46 p.m.