summary.data {MSstatsPTM} | R Documentation

## 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)

[Package MSstatsPTM version 1.4.2 Index]