Prepare feature-level data for protein-level summarization

Prepare feature-level data for protein-level summarization

MSstatsPrepareForSummarization(
  input,
  method,
  impute,
  censored_symbol,
  remove_uninformative_feature_outlier
)

Arguments

input

feature-level data processed by dataProcess subfunctions
method

summarization method - `summaryMethod` parameter of the dataProcess function
impute

if TRUE, censored missing values will be imputed - `MBimpute` parameter of the dataProcess function
censored_symbol

censored missing value indicator - `censoredInt` parameter of the dataProcess function
remove_uninformative_feature_outlier

if TRUE, features labeled as outlier of uninformative by the MSstatsSelectFeatures function will not be used in summarization

Value

data.table

Examples

raw = DDARawData
method = "TMP"
cens = "NA"
impute = TRUE
MSstatsConvert::MSstatsLogsSettings(FALSE)
input = MSstatsPrepareForDataProcess(raw, 2, NULL)
#> INFO  [2021-07-05 20:05:28] ** Features with one or two measurements across runs are removed.
#> INFO  [2021-07-05 20:05:28] ** Fractionation handled.
#> INFO  [2021-07-05 20:05:28] ** Updated quantification data to make balanced design. Missing values are marked by NA
head(input)
#>    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                G.PLTGTYR_8_8      NA_NA
#> 5:  bovine       H.SFNVEYDDSQDK_465_465      NA_NA
#> 6:  bovine        K.AVVQDPALKPL_156_156      NA_NA
#>                               FEATURE LABEL GROUP_ORIGINAL SUBJECT_ORIGINAL RUN
#> 1:             D.GPLTGTYR_23_23_NA_NA     L             C1                1   1
#> 2: F.HFHWGSSDDQGSEHTVDR_402_402_NA_NA     L             C1                1   1
#> 3:   F.HWGSSDDQGSEHTVDR_229_229_NA_NA     L             C1                1   1
#> 4:                G.PLTGTYR_8_8_NA_NA     L             C1                1   1
#> 5:       H.SFNVEYDDSQDK_465_465_NA_NA     L             C1                1   1
#> 6:        K.AVVQDPALKPL_156_156_NA_NA     L             C1                1   1
#>    GROUP SUBJECT FRACTION INTENSITY ABUNDANCE originalRUN
#> 1:     1       1        1  757400.1  19.53070           1
#> 2:     1       1        1 2087125.8  20.99309           1
#> 3:     1       1        1 1485145.8  20.50217           1
#> 4:     1       1        1 4986404.0  22.24957           1
#> 5:     1       1        1 2488141.2  21.24664           1
#> 6:     1       1        1 7519322.0  22.84217           1