removeSampleInList

(integer) column number to exclude

remSamp

(character) names of list-elements where columns indicated with 'remSamp' should be removed

listElem

silent

(character) allows easier tracking of messages produced

callFrom

Remove samples/columns from list of matrixes 
Remove samples (ie columns) from every instance of list of matrixes.
Note: This function assumes same order of columns in list-elements 'listElem' !

Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Quantitative proteomics measurements frequently contain multiple NA values, due to physical absence of given peptides in some samples, limitations in sensitivity or other reasons.
The functions provided here help to inspect graphically the data to investigate the nature of NA-values via their respective replicate measurements and to help/confirm the choice of NA-replacement by low random values.
Dedicated filtering and statistical testing using the framework of package 'limma' <doi:10.18129/B9.bioc.limma> can be run, enhanced by multiple rounds of NA-replacements to provide robustness towards rare stochastic events.
Multi-species samples, as frequently used in benchmark-tests (eg Navarro et al 2016 <doi:10.1038/nbt.3685>, Ramus et al 2016 <doi:10.1016/j.jprot.2015.11.011>), can be run with special options separating the data into sub-groups during normalization and testing.
As example the data-set from Ramus et al 2016 <doi:10.1016/j.jprot.2015.11.011>) is provided quantified by MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), ProteomeDiscoverer,
OpenMS (<doi:10.1038/nmeth.3959>) and Proline (Bouyssie et al 2020 <doi:10.1093/bioinformatics/btaa118>).
Subsequently, ROC curves (Hand and Till 2001 <doi:10.1023/A:1010920819831>) can be constructed to compare multiple analysis approaches.

Wolfgang Raffelsberger

wrProteo

Proteomics Data Analysis Functions

removeSampleInList function

Remove samples/columns from list of matrixes
  
Remove samples (ie columns) from every instance of list of matrixes.
Note: This function assumes same order of columns in list-elements 'listElem' ! — removeSampleInList

Remove samples/columns from list of matrixes
  
Remove samples (ie columns) from every instance of list of matrixes.
Note: This function assumes same order of columns in list-elements 'listElem' !

removeSampleInList: Remove samples/columns from list of matrixes Remove samples (ie columns) from every instance of list of matrixes. Note: This function assumes same order of columns in list-elements 'listElem' !

Description

Usage

Arguments

Value

See Also

Examples