MSstatsLiP_Summarized {MSstatsLiP} | R Documentation

## MSstatsLiP_Summarized

### Description

Example output of MSstatsLiP summarization function dataSummarizationLiP.

### Usage

    MSstatsLiP_Summarized

### Format

A list containing two lists of summarization information for LiP and TrP data.

### Details

Example output of MSstatsLiP summarization function dataSummarizationLiP. A list containing two lists named LiP and TrP containing summarization information for LiP and TrP data. Each of LiP and TrP contain data named: FeatureLevelData, ProteinLevelData, SummaryMethod, ModelQC, PredictBySurvival. The two main data.tables (FeatureLevelData and ProteinLevelData are shown below):

- FeatureLevelData :

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

  - FULL_PEPTIDE (LiP Only) : Combined name of protein and peptide sequence

  - 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 : Original intensity value

  - ABUNDANCE : Log adjusted intensity value

  - newABUNDANCE : Normalized abundance column

- ProteinLevelData :

  - RUN : MS run ID

  - FULL_PEPTIDE (LiP Only) : Combined name of protein and peptide sequence

  - 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.

### Examples

    head(MSstatsLiP_Summarized$LiP$FeatureLevelData)
    head(MSstatsLiP_Summarized$LiP$ProteinLevelData)

    head(MSstatsLiP_Summarized$TrP$FeatureLevelData)
    head(MSstatsLiP_Summarized$TrP$ProteinLevelData)

[Package MSstatsLiP version 1.0.0 Index]