Prepare output for dataProcess for group comparison

Prepare output for dataProcess for group comparison

MSstatsPrepareForGroupComparison(summarization_output)

Arguments

summarization_output	output of dataProcess

Value

list of run-level data for each protein in the input. This list has a "has_imputed" attribute that indicates if missing values were imputed in the input dataset.

Examples

QuantData <- dataProcess(SRMRawData, use_log_file = FALSE)
#> 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
#> INFO  [2021-07-05 20:05:28] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
#> INFO  [2021-07-05 20:05:28] ** Log2 intensities = NA were considered as censored missing values.
#> INFO  [2021-07-05 20:05:28] ** Use all features that the dataset originally has.
#> INFO  [2021-07-05 20:05:28] 
#>  # proteins: 2
#>  # peptides per protein: 2-2
#>  # features per peptide: 3-3
#> INFO  [2021-07-05 20:05:28] 
#>                     1 2 3 4 5 6 7 8 9 10
#>              # runs 3 3 3 3 3 3 3 3 3  3
#>     # bioreplicates 3 3 3 3 3 3 3 3 3  3
#>  # tech. replicates 1 1 1 1 1 1 1 1 1  1
#> INFO  [2021-07-05 20:05:28]  == Start the summarization per subplot...
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
#> INFO  [2021-07-05 20:05:28]  == Summarization is done.
group_comparison_input = MSstatsPrepareForGroupComparison(QuantData)
length(group_comparison_input) # list of length equal to number of proteins
#> [1] 2
# in protein-level data of QuantData
head(group_comparison_input[[1]])
#>    RUN Protein LogIntensities originalRUN GROUP SUBJECT TotalGroupMeasurements
#> 1:   1    IDHC       5.577050           1     1   ReplA                     18
#> 2:   2    IDHC       6.811034           2     1   ReplB                     18
#> 3:   3    IDHC       6.909093           3     1   ReplC                     18
#> 4:   4    IDHC       6.373069           4     2   ReplA                     18
#> 5:   5    IDHC       6.595750           5     2   ReplB                     18
#> 6:   6    IDHC       6.349843           6     2   ReplC                     18
#>    NumMeasuredFeature MissingPercentage more50missing NumImputedFeature
#> 1:                  6                 0         FALSE                 0
#> 2:                  6                 0         FALSE                 0
#> 3:                  6                 0         FALSE                 0
#> 4:                  6                 0         FALSE                 0
#> 5:                  6                 0         FALSE                 0
#> 6:                  6                 0         FALSE                 0