Handle censored missing values

Handle censored missing values

MSstatsHandleMissing(
  input,
  summary_method,
  impute,
  missing_symbol,
  censored_cutoff
)

Arguments

input

`data.table` in MSstats data format
summary_method

summarization method (`summaryMethod` parameter to `dataProcess`)
impute

if TRUE, missing values are supposed to be imputed (`MBimpute` parameter to `dataProcess`)
missing_symbol

`censoredInt` parameter to `dataProcess`
censored_cutoff

`maxQuantileforCensored` parameter to `dataProcess`

Value

data.table

Examples

raw = DDARawData
method = "TMP"
cens = "NA"
impute = TRUE
MSstatsConvert::MSstatsLogsSettings(FALSE)
input = MSstatsPrepareForDataProcess(raw, 2, NULL)
#> INFO  [2021-07-05 20:05:27] ** Features with one or two measurements across runs are removed.
#> INFO  [2021-07-05 20:05:27] ** Fractionation handled.
#> INFO  [2021-07-05 20:05:27] ** 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 20:05:27] ** Log2 intensities under cutoff = 13.456  were considered as censored missing values.
#> INFO  [2021-07-05 20:05:27] ** Log2 intensities = NA were considered as censored missing values.
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 censored
#> 1:     1       1        1  757400.1  19.83052           1    FALSE
#> 2:     1       1        1 2087125.8  21.29291           1    FALSE
#> 3:     1       1        1 1485145.8  20.80200           1    FALSE
#> 4:     1       1        1 4986404.0  22.54939           1    FALSE
#> 5:     1       1        1 2488141.2  21.54646           1    FALSE
#> 6:     1       1        1 7519322.0  23.14200           1    FALSE