summary.data.tmt: Example of output from dataSummarizationPTM_TMT function for...

In Vitek-Lab/MSstatsPTM: Statistical Characterization of Post-translational Modifications

Example of output from dataSummarizationPTM_TMT function for TMT data

Description

It is made from raw.input.tmt. It is the output of dataSummarizationPTM_TMT function from MSstatsPTM. It should include a list with two names PTM and PROTEIN. Each of these list values is also a list with two names ProteinLevelData and FeatureLevelData, which correspond to two data.tables.The columns in these two data.tables are listed below. The variables are as follows:

• FeatureLevelData :

  • ProteinName : MS run ID

  • PSM : Protein ID with modification site mapped in. Ex. Protein_1002_S836

  • censored: Protein-level summarized abundance

  • predicted : Labeling information (126, ... 131)

  • log2Intensity : Condition (ex. Healthy, Cancer, Time0)

  • Run : Unique ID for biological subject.

  • Channel : Unique ID for technical replicate of one TMT mixture.

  • BioReplicate : Unique ID for TMT mixture.

  • Condition : Unique ID for TMT mixture.

  • Mixture : Unique ID for TMT mixture.

  • TechRepMixture : Unique ID for TMT mixture.

  • PeptideSequence : Unique ID for TMT mixture.

  • Charge : Unique ID for TMT mixture.

• ProteinLevelData :

  • Mixture : MS run ID

  • TechRepMixture : Protein ID with modification site mapped in. Ex. Protein_1002_S836

  • Run: Protein-level summarized abundance

  • Channel : Labeling information (126, ... 131)

  • Protein : Condition (ex. Healthy, Cancer, Time0)

  • Abundance : Unique ID for biological subject.

  • BioReplicate : Unique ID for technical replicate of one TMT mixture.

  • Condition : Unique ID for TMT mixture.

Usage

summary.data.tmt

Format

A list of two lists with four data.tables.

Examples

head(summary.data.tmt)

Vitek-Lab/MSstatsPTM documentation built on Sept. 26, 2024, 9:28 p.m.