MetProc: Separate Metabolites into Likely Measurement Artifacts and True Metabolites

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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.

Author
Mark Chaffin
Date of publication
2016-05-19 05:46:39
Maintainer
Mark Chaffin <mac8278@mail.harvard.edu>
License
GPL (>= 2)
Version
1.0.1

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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

Files in this package

MetProc
MetProc/inst
MetProc/inst/extdata
MetProc/inst/extdata/sampledata.csv
MetProc/inst/doc
MetProc/inst/doc/using-MetProc.html
MetProc/inst/doc/using-MetProc.R
MetProc/inst/doc/using-MetProc.Rmd
MetProc/NAMESPACE
MetProc/R
MetProc/R/functions_cleane.R
MetProc/vignettes
MetProc/vignettes/using-MetProc.Rmd
MetProc/vignettes/pp_bio_corr.png
MetProc/vignettes/removed.png
MetProc/vignettes/metrics.png
MetProc/vignettes/retained.png
MetProc/MD5
MetProc/build
MetProc/build/vignette.rds
MetProc/DESCRIPTION
MetProc/man
MetProc/man/sampledata.Rd
MetProc/man/MetProc-package.Rd
MetProc/man/subset_met.Rd
MetProc/man/heatmap_res.Rd
MetProc/man/run_metric.Rd
MetProc/man/met_proc.Rd
MetProc/man/get_missing.Rd
MetProc/man/plot_pp_sample_missing.Rd
MetProc/man/write.met.Rd
MetProc/man/corr_metric.Rd
MetProc/man/get_group.Rd
MetProc/man/plot_metric.Rd
MetProc/man/read.met.Rd