Get feature-level data to be used in the MSstatsSummarizationOutput function

Get feature-level data to be used in the MSstatsSummarizationOutput function

getProcessed(input)

Arguments

input	data.table processed by dataProcess subfunctions

Value

data.table processed by dataProcess subfunctions

Examples

raw = DDARawData
method = "TMP"
cens = "NA"
impute = TRUE
MSstatsConvert::MSstatsLogsSettings(FALSE)
input = MSstatsPrepareForDataProcess(raw, 2, NULL)
#> INFO  [2021-07-05 20:05:57] ** Features with one or two measurements across runs are removed.
#> INFO  [2021-07-05 20:05:57] ** Fractionation handled.
#> INFO  [2021-07-05 20:05:57] ** Updated quantification data to make balanced design. Missing values are marked by NA
input = MSstatsNormalize(input, "EQUALIZEMEDIANS")
input = MSstatsMergeFractions(input)
input = MSstatsHandleMissing(input, "TMP", TRUE, "NA", 0.999)
#> INFO  [2021-07-05 20:05:57] ** Log2 intensities under cutoff = 13.456  were considered as censored missing values.
#> INFO  [2021-07-05 20:05:57] ** Log2 intensities = NA were considered as censored missing values.
input_all = MSstatsSelectFeatures(input, "all") # all features
#> INFO  [2021-07-05 20:05:57] ** Use all features that the dataset originally has.
input_5 = MSstatsSelectFeatures(data.table::copy(input),
"topN", top_n = 5) # top 5 features
#> INFO  [2021-07-05 20:05:57] ** Use top5 features that have highest average of log2(intensity) across runs.

proc1 = getProcessed(input_all)
proc2 = getProcessed(input_5)

proc1
#> NULL
proc2
#>       PROTEIN                      PEPTIDE TRANSITION
#>    1:  bovine             D.GPLTGTYR_23_23      NA_NA
#>    2:  bovine F.HFHWGSSDDQGSEHTVDR_402_402      NA_NA
#>    3:  bovine   F.HWGSSDDQGSEHTVDR_229_229      NA_NA
#>    4:  bovine       H.SFNVEYDDSQDK_465_465      NA_NA
#>    5:  bovine     K.KYAAELHLVHWNTK_700_700      NA_NA
#>   ---                                                
#> 1526:   yeast         K.GVIFYESHGK_144_144      NA_NA
#> 1527:   yeast       K.SISIVGSYVGNR_273_273      NA_NA
#> 1528:   yeast      L.GIDGGEGKEELFR_408_408      NA_NA
#> 1529:   yeast            L.STLPEIYEK_97_97      NA_NA
#> 1530:   yeast      R.VLGIDGGEGKEELFR_98_98      NA_NA
#>                                  FEATURE LABEL GROUP_ORIGINAL SUBJECT_ORIGINAL
#>    1:             D.GPLTGTYR_23_23_NA_NA     L             C1                1
#>    2: F.HFHWGSSDDQGSEHTVDR_402_402_NA_NA     L             C1                1
#>    3:   F.HWGSSDDQGSEHTVDR_229_229_NA_NA     L             C1                1
#>    4:       H.SFNVEYDDSQDK_465_465_NA_NA     L             C1                1
#>    5:     K.KYAAELHLVHWNTK_700_700_NA_NA     L             C1                1
#>   ---                                                                         
#> 1526:         K.GVIFYESHGK_144_144_NA_NA     L             C6                1
#> 1527:       K.SISIVGSYVGNR_273_273_NA_NA     L             C6                1
#> 1528:      L.GIDGGEGKEELFR_408_408_NA_NA     L             C6                1
#> 1529:            L.STLPEIYEK_97_97_NA_NA     L             C6                1
#> 1530:      R.VLGIDGGEGKEELFR_98_98_NA_NA     L             C6                1
#>       RUN GROUP SUBJECT FRACTION INTENSITY ABUNDANCE originalRUN censored
#>    1:   1     1       1        1  757400.1  19.83052           1    FALSE
#>    2:   1     1       1        1 2087125.8  21.29291           1    FALSE
#>    3:   1     1       1        1 1485145.8  20.80200           1    FALSE
#>    4:   1     1       1        1 2488141.2  21.54646           1    FALSE
#>    5:   1     1       1        1 1018682.2  20.25810           1    FALSE
#>   ---                                                                    
#> 1526:  18     6       1        1        NA        NA          18     TRUE
#> 1527:  18     6       1        1        NA        NA          18     TRUE
#> 1528:  18     6       1        1        NA        NA          18     TRUE
#> 1529:  18     6       1        1        NA        NA          18     TRUE
#> 1530:  18     6       1        1        NA        NA          18     TRUE
#>       remove
#>    1:   TRUE
#>    2:   TRUE
#>    3:   TRUE
#>    4:   TRUE
#>    5:   TRUE
#>   ---       
#> 1526:   TRUE
#> 1527:   TRUE
#> 1528:   TRUE
#> 1529:   TRUE
#> 1530:   TRUE