R/groupComparisonPTM.R
groupComparisonPTM.Rd
Takes summarized PTM and protein data from proteinSummarization. If protein data is unavailable, PTM data only can be passed into the function. Including protein data allows for adjusting PTM Fold Change by the change in protein abundance without modification.
groupComparisonPTM( data, data.type, contrast.matrix = "pairwise", moderated = FALSE, adj.method = "BH" )
data | list of summarized datasets. Output of MSstatsPTM summarization
function |
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data.type | string indicating experimental acquisition type. "TMT" is used for TMT labeled experiments. For all other experiments (Label Free/ DDA/ DIA) use "LabelFree". |
contrast.matrix | comparison between conditions of interests. Default models full pairwise comparison between all conditions |
moderated | For TMT experiments only. TRUE will moderate t statistic; FALSE (default) uses ordinary t statistic. Default is FALSE. |
adj.method | For TMT experiemnts only. Adjusted method for multiple comparison. "BH" is default. "BH" is used for all other experiment types |
list of modeling results. Includes PTM, PROTEIN, and ADJUSTED data.tables with their corresponding model results.
#> # A tibble: 6 x 10 #> ProteinName PeptideSequence Condition BioReplicate Run Intensity #> <chr> <chr> <chr> <chr> <chr> <dbl> #> 1 Q9UHD8_K262 DAGLK*QAPASR CCCP BCH1 CCCP-B1T1 1423906. #> 2 Q9UHD8_K262 DAGLK*QAPASR CCCP BCH1 CCCP-B1T2 877045. #> 3 Q9UHD8_K262 DAGLK*QAPASR CCCP BCH2 CCCP-B2T1 384418. #> 4 Q9UHD8_K262 DAGLK*QAPASR CCCP BCH2 CCCP-B2T2 454858. #> 5 Q9UHD8_K262 DAGLK*QAPASR Combo BCH1 Combo-B1T1 1603377. #> 6 Q9UHD8_K262 DAGLK*QAPASR Combo BCH1 Combo-B1T2 676555. #> # ... with 4 more variables: PrecursorCharge <chr>, FragmentIon <lgl>, #> # ProductCharge <lgl>, IsotopeLabelType <chr>#> # A tibble: 6 x 10 #> ProteinName PeptideSequence Condition BioReplicate Run Intensity #> <chr> <chr> <chr> <chr> <chr> <dbl> #> 1 Q9UHD8 STLINTLFK CCCP BCH2 CCCP-B2T1 367944. #> 2 Q9UHD8 STLINTLFK CCCP BCH2 CCCP-B2T2 341207. #> 3 Q9UHD8 STLINTLFK Combo BCH2 Combo-B2T1 185843. #> 4 Q9UHD8 STLINTLFK Ctrl BCH2 Ctrl-B2T1 529224. #> 5 Q9UHD8 STLINTLFK Ctrl BCH2 Ctrl-B2T2 483355. #> 6 Q9UHD8 STLINTLFK USP30_OE BCH2 USP30_OE-B2T1 447795. #> # ... with 4 more variables: PrecursorCharge <chr>, FragmentIon <lgl>, #> # ProductCharge <lgl>, IsotopeLabelType <chr>#>#> INFO [2021-04-30 11:44:35] ** Features with one or two measurements across runs are removed. #> INFO [2021-04-30 11:44:35] ** Fractionation handled. #> INFO [2021-04-30 11:44:35] ** Updated quantification data to make balanced design. Missing values are marked by NA #> INFO [2021-04-30 11:44:35] ** Log2 intensities under cutoff = 13.751 were considered as censored missing values. #> INFO [2021-04-30 11:44:35] ** Log2 intensities = NA were considered as censored missing values. #> INFO [2021-04-30 11:44:35] ** Use all features that the dataset originally has. #> INFO [2021-04-30 11:44:35] #> # proteins: 125 #> # peptides per protein: 1-5 #> # features per peptide: 1-1 #> INFO [2021-04-30 11:44:35] Five or more proteins have only one feature: #> Q9UHD8_K028, #> Q9UHD8_K069, #> Q9UHD8_K141, #> Q9UHQ9_K046, #> Q9UHQ9_K062 ... #> INFO [2021-04-30 11:44:35] #> CCCP Combo Ctrl USP30_OE #> #> # runs 4 4 4 4 #> #> # bioreplicates 2 2 2 2 #> #> # tech. replicates 2 2 2 2 #> INFO [2021-04-30 11:44:35] Five or more features are completely missing in at least one condition, #> VYLK*GVHPK_2_NA_NA, #> GVHPK*FPEGGK_2_NA_NA, #> MSQYLDSLK*VGDVVEFR_3_NA_NA, #> DWAYSK*GFVTADMIR_2_NA_NA, #> DWAYSK*GFVTADMIR_3_NA_NA #> INFO [2021-04-30 11:44:35] #> == Start the summarization per subplot... #> | | | 0% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |=== | 4% | |=== | 5% | |==== | 6% | |===== | 7% | |====== | 8% | |====== | 9% | |======= | 10% | |======== | 11% | |======== | 12% | |========= | 13% | |========== | 14% | |=========== | 15% | |=========== | 16% | |============ | 17% | |============ | 18% | |============= | 18% | |============= | 19% | |============== | 20% | |=============== | 21% | |=============== | 22% | |================ | 22% | |================ | 23% | |================= | 24% | |================= | 25% | |================== | 26% | |=================== | 27% | |==================== | 28% | |==================== | 29%#> Warning: Ran out of iterations and did not converge#> | |===================== | 30% | |====================== | 31% | |====================== | 32% | |======================= | 33% | |======================== | 34% | |========================= | 35% | |========================= | 36% | 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|===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100%INFO [2021-04-30 11:44:36] == the summarization per subplot is done.#>#> INFO [2021-04-30 11:44:36] ** Features with one or two measurements across runs are removed. #> INFO [2021-04-30 11:44:36] ** Fractionation handled. #> INFO [2021-04-30 11:44:36] ** Updated quantification data to make balanced design. Missing values are marked by NA #> INFO [2021-04-30 11:44:36] ** Log2 intensities under cutoff = 16.998 were considered as censored missing values. #> INFO [2021-04-30 11:44:36] ** Log2 intensities = NA were considered as censored missing values. #> INFO [2021-04-30 11:44:36] ** Use all features that the dataset originally has. #> INFO [2021-04-30 11:44:36] #> # proteins: 26 #> # peptides per protein: 1-9 #> # features per peptide: 1-1 #> INFO [2021-04-30 11:44:36] Five or more proteins have only one feature: #> Q9UHD8, #> Q9UHQ9, #> Q9UIF8, #> Q9UL25, #> Q9UNH7 ... #> INFO [2021-04-30 11:44:36] #> CCCP Combo Ctrl USP30_OE #> #> # runs 4 4 4 4 #> #> # bioreplicates 2 2 2 2 #> #> # tech. replicates 2 2 2 2 #> INFO [2021-04-30 11:44:36] Five or more features are completely missing in at least one condition, #> TVYSHLFDHVVNR_4_NA_NA, #> TDQFPLFLIIMGK_2_NA_NA, #> LMKMAR_2_NA_NA, #> TVYSHLFDHVVNR_4_NA_NA, #> TDQFPLFLIIMGK_2_NA_NA #> INFO [2021-04-30 11:44:36] #> == Start the summarization 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|============================================================== | 88% | |================================================================= | 92% | |=================================================================== | 96% | |======================================================================| 100%INFO [2021-04-30 11:44:37] == the summarization per subplot is done.model.lf.msstatsptm <- groupComparisonPTM(quant.lf.msstatsptm, data.type = "LabelFree")#>#> | | | 0% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |=== | 4% | |=== | 5% | |==== | 6% | |===== | 7% | |====== | 8% | |====== | 9% | |======= | 10% | |======== | 11% | |======== | 12% | |========= | 13% | |========== | 14% | |=========== | 15% | |=========== | 16% | |============ | 17% | |============ | 18% | |============= | 18% | |============= | 19% | |============== | 20% | |=============== | 21% | |=============== | 22% | |================ | 22% | |================ | 23% | |================= | 24% | |================= | 25% | 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