LiP Significance Analysis in shotgun mass spectrometry-based
proteomic experiments
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Documentation for package ‘MSstatsLiP’ version 1.0.0
Help Pages
| annotSite | Annotate modification site |
| BarcodePlotLiP | Barcode plot. Shows protein coverge of LiP modified peptides. |
| calculateTrypticity | Calculates level of trypticity for a list of LiP Peptides. |
| correlationPlotLiP | Plot run correlation for provided LiP and TrP experiment. |
| dataProcessPlotsLiP | Visualization for explanatory data analysis |
| dataSummarizationLiP | Summarizes LiP and TrP datasets seperately using methods from MSstats. |
| groupComparisonLiP | Model LiP and TrP data and make adjustments if needed Returns list of three modeled datasets |
| groupComparisonPlotsLiP | Visualization for model-based analysis and summarization |
| LiPRawData | LiPRawData |
| locateMod | Locate modified sites with a peptide |
| locatePTM | Annotate modified sites with associated peptides |
| MSstatsLiP | MSstatsLiP: A package for identifying and analyzing changes in protein structures caused by compound binding in cellur lysates. |
| MSstatsLiP_data | MSstatsLiP_data |
| MSstatsLiP_model | MSstatsLiP_model |
| MSstatsLiP_Summarized | MSstatsLiP_Summarized |
| PCAPlotLiP | Visualize PCA analysis for LiP and TrP datasets. |
| SkylineTest | SkylineTest |
| SkylinetoMSstatsLiPFormat | Converts raw LiP MS data from Skyline into the format needed for MSstatsLiP. |
| SpectronauttoMSstatsLiPFormat | Converts raw LiP MS data from Spectronautt into the format needed for MSstatsLiP. |
| tidyFasta | Read and tidy a FASTA file |
| TrPRawData | TrPRawData |
| trypticHistogramLiP | Histogram of Half vs Fully tryptic peptides. Calculates proteotypicity, and then uses calcualtions in histogram. |