MSstatsLiP_model: MSstatsLiP_model

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

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)

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