MSstatsLiP_Summarized: MSstatsLiP_Summarized

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

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)

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