romicsOutlierRemove: Romics_outlier_remove()

In PNNL-Comp-Mass-Spec/RomicsProcessor: omics-oriented package for reproducible and sharable data processing pipelines

Romics_outlier_remove()

Description

Removes outliers below a certain pvalue threshold. The pmartR method for the removal of outliers is used (require the installation of the package pmartR). The evaluation of the outlier removal can be done prior to apply this function using the function Romics_outlier_eval().

Usage

romicsOutlierRemove(
  romics_object,
  seed = 42,
  metrics = c("Correlation", "Proportion_Missing", "MAD", "Skewness"),
  pvalue_threshold = 0.01
)

Arguments

romics_object	A log transformed romics_object created using romicsCreateObject() and transformed using the function log2transform() or log10transform()
seed	An integer of length 1, by default 42 will be used
metrics	A character vector containing the following terms to indicate which parameters to use for the filtering of the data : 'Correlation', 'Proportion_Missing','MAD', 'Skewness'. By defaults all parameters will be used.
pvalue_threshold	A numeric vector of lenght 1 indicating the pvalue threshold to be used.

Details

This function requires the package 'pmartR' to be installed and loaded to be excecuted. It will calculate and plot the samples to be filtered out using the function Romics_outlier_eval().

Value

This function will print the pmartR filtering details and will return 2 plots the first one is a scatter plot of the pvalue by log2(Robust Mahalanobis Distance) the second one is a scatter plot of the log2(Robust Mahalanobis Distance) per sample.

Author(s)

Geremy Clair

References

Matzke, M., Waters, K., Metz, T., Jacobs, J., Sims, A., Baric, R., Pounds, J., and Webb-Robertson, B.J. (2011), Improved quality control processing of peptide-centric LC-MS proteomics data. Bioinformatics. 27(20): 2866-2872.

PNNL-Comp-Mass-Spec/RomicsProcessor documentation built on March 18, 2023, 5:14 a.m.