MSstatsLiP_model {MSstatsLiP} | R Documentation

## MSstatsLiP_model

### Description

Example output of groupComparisonLiP converter functions.

### Usage

    MSstatsLiP_model

### Format

A data.table consisting of 546 rows and 29 columns. Raw TrP data for use in testing and examples.

### Details

Example output of MSstatsLiP groupComparisonLiP function. A list containing three data.tables corresponding to unadjusted LiP, TrP, and adjusted LiP models. The data.tables contain the following columns:

- ProteinName : Character column of protein names

- PeptideSequence : Character column of peptide sequence name

- Label : Condition comparison (Eg. Disease vs Control)

- log2FC : Fold Change output results of model

- SE : Standard error output of model

- Tvalue : Tvalue output of model

- DF : Degrees of Freedom output of model

- pvalue : Pvalue result of model (unadjusted)

- adj.pvalue : Adjusted Pvalue, generally BH adjustement is used

- issue : Issue in model if any is reported

- MissingPercentage : Percent of missing values in specific model

- ImputationPercentage : Percent of values that needed to be imputed

- fully_TRI: Boolean indicating if Peptide is fully tryptic

- NSEMI_TRI: Boolean indicating if Peptide is NSEMI tryptic

- CSEMI_TRI: Boolean indicating if Peptide is CSEMI tryptic

- CTERMINUS: Boolean indicating if Peptide is CTERMINUS tryptic

- NTERMINUS: Boolean indicating if Peptide is NTERMINUS tryptic

- StartPos: Start position of peptide sequence

- EndPos: End position of peptide sequence

- FULL_PEPTIDE(LiP data only) : Combined protein name and peptide sequence. Used for LiP data only because LiP is summarized to peptide level (not protein)

### Examples

    head(MSstatsLiP_model$LiP.Model)
    head(MSstatsLiP_model$TrP.Model)
    head(MSstatsLiP_model$Adjusted.LiP.Model)

[Package MSstatsLiP version 1.0.0 Index]