summary.data: Example of output from dataSummarizationPTM function for...

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

Example of output from dataSummarizationPTM function for non-TMT data

Description

It is made from raw.input. It is the output of dataSummarizationPTM 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 :

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

  • PEPTIDE : Full peptide with charge

  • TRANSITION: Charge

  • FEATURE : Combination of Protien, Peptide, and Transition Columns

  • LABEL :

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

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

  • SUBJECT : Unique ID for biological subject.

  • FRACTION : Unique Fraction ID

  • originalRUN : Run name

  • censored :

  • INTENSITY : Unique ID for TMT mixture.

  • ABUNDANCE : Unique ID for TMT mixture.

  • newABUNDANCE : Unique ID for TMT mixture.

  • predicted : Unique ID for TMT mixture.

• ProteinLevelData :

  • RUN : MS run ID

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

  • LogIntensities: Protein-level summarized abundance

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

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

  • SUBJECT : Unique ID for biological subject.

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

  • NumMeasuredFeature : Unique ID for TMT mixture.

  • MissingPercentage : Unique ID for TMT mixture.

  • more50missing : Unique ID for TMT mixture.

  • NumImputedFeature : Unique ID for TMT mixture.

Usage

summary.data

Format

A list of two lists with four data.tables.

Examples

head(summary.data)

Vitek-Lab/MSstatsPTM documentation built on Dec. 19, 2024, 6:02 a.m.