proteinSummarization.Rd
We assume missing values are censored and then impute the missing values. Protein-level summarization from peptide level quantification are performed. After all, global median normalization on peptide level data and normalization between MS runs using reference channels will be implemented.
proteinSummarization( data, method = "msstats", global_norm = TRUE, reference_norm = TRUE, remove_norm_channel = TRUE, remove_empty_channel = TRUE, MBimpute = TRUE, maxQuantileforCensored = NULL )
data | Name of the output of PDtoMSstatsTMTFormat function or peptide-level quantified data from other tools. It should have columns ProteinName, PeptideSequence, Charge, PSM, Mixture, TechRepMixture, Run, Channel, Condition, BioReplicate, Intensity |
---|---|
method | Four different summarization methods to protein-level can be performed : "msstats"(default), "MedianPolish", "Median", "LogSum". |
global_norm | Global median normalization on peptide level data (equalizing the medians across all the channels and MS runs). Default is TRUE. It will be performed before protein-level summarization. |
reference_norm | Reference channel based normalization between MS runs on protein level data. TRUE(default) needs at least one reference channel in each MS run, annotated by 'Norm' in Condtion column. It will be performed after protein-level summarization. FALSE will not perform this normalization step. If data only has one run, then reference_norm=FALSE. |
remove_norm_channel | TRUE(default) removes 'Norm' channels from protein level data. |
remove_empty_channel | TRUE(default) removes 'Empty' channels from protein level data. |
MBimpute | only for method="msstats". TRUE (default) imputes missing values by Accelated failure model. FALSE uses minimum value to impute the missing value for each peptide precursor ion. |
maxQuantileforCensored | We assume missing values are censored. maxQuantileforCensored is Maximum quantile for deciding censored missing value, for instance, 0.999. Default is Null. |
data.frame with protein-level summarization for each run and channel
data(input.pd) quant.pd.msstats <- proteinSummarization(input.pd, method="msstats", global_norm=TRUE, reference_norm=TRUE)#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 4-29 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 3-33 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 3-29 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 1-28 #> # of Transitions/Peptide 1-1#> #>#> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 1-30 #> # of Transitions/Peptide 1-1#> #>#> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 2-30 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 4-31 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 3-30 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 5-30 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 3-31 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 3-31 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 1-31 #> # of Transitions/Peptide 1-1#> #>#> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 3-34 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 2-30 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 5-32 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#>#>#>#>#>#>#>#>#> Run Protein Abundance Channel #> 1 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw P04406 16.59812 127C #> 2 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw P04406 16.55729 129N #> 3 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw P04406 16.71783 128N #> 4 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw P04406 16.67190 129C #> 5 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw P04406 16.51106 127N #> 6 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw P04406 16.49448 130C #> BioReplicate Condition TechRepMixture Mixture #> 1 Mixture1_0.125 0.125 1 Mixture1 #> 2 Mixture1_0.125 0.125 1 Mixture1 #> 3 Mixture1_0.5 0.5 1 Mixture1 #> 4 Mixture1_0.5 0.5 1 Mixture1 #> 5 Mixture1_0.667 0.667 1 Mixture1 #> 6 Mixture1_0.667 0.667 1 Mixture1