MSstatsLiP_data: MSstatsLiP_data

In devonjkohler/MSstatsLiP: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Description

Example output of MSstatsLiP converter functions.

Usage

MSstatsLiP_data

Format

A data.table consisting of 546 rows and 29 columns. Raw TrP data for use in testing and examples.

Details

Example output of MSstatsLiP converter functions. (Eg. SpectronauttoMSstatsLiPFormat). A list containing two data.tables named LiP and TrP corresponding to the processed LiP and TrP data now in MSstatsLiP format. The data.tables contain the following columns:

• ProteinName : Character column of protein names

• PeptideSequence : Character column of peptide sequence name

• PrecursorCharge : Numeric charge feature

• FragmentIon : Character fragment ion feature

• ProductCharge : Numeric charge of product

• IsotopeLabelType : Character label type

• Condition : Character label for condition (Eg. Disease/Control)

• BioReplicate : Name of biological replicate

• Run : Name of run

• Fraction : Fraction number if fractionation is present

• Intensity : Unnormalized feature intensity

• FULL_PEPTIDE(LiP data only) : Combined protein name and peptide sequence. Used for LiP data only because LiP is summarized to peptide level (not protein)

Examples

head(MSstatsLiP_data$LiP)
head(MSstatsLiP_data$TrP)

devonjkohler/MSstatsLiP documentation built on Dec. 19, 2021, 11:01 p.m.