impute | R Documentation |
impute
is calculating imputation values for missing data depending on the selected
method.
impute( data, sample, grouping, intensity_log2, condition, comparison = comparison, missingness = missingness, noise = NULL, method = "ludovic", skip_log2_transform_error = FALSE, retain_columns = NULL )
data |
a data frame that is ideally the output from the |
sample |
a character column in the |
grouping |
a character column in the |
intensity_log2 |
a numeric column in the |
condition |
a character or numeric column in the |
comparison |
a character column in the |
missingness |
a character column in the |
noise |
a numeric column in the |
method |
a character value that specifies the method to be used for imputation. For
|
skip_log2_transform_error |
a logical value that determines if a check is performed to validate that input values are log2 transformed. If input values are > 40 the test is failed and an error is returned. |
retain_columns |
a vector that indicates columns that should be retained from the input
data frame. Default is not retaining additional columns |
A data frame that contains an imputed_intensity
and imputed
column in
addition to the required input columns. The imputed
column indicates if a value was
imputed. The imputed_intensity
column contains imputed intensity values for previously
missing intensities.
set.seed(123) # Makes example reproducible # Create example data data <- create_synthetic_data( n_proteins = 10, frac_change = 0.5, n_replicates = 4, n_conditions = 2, method = "effect_random", additional_metadata = FALSE ) head(data, n = 24) # Assign missingness information data_missing <- assign_missingness( data, sample = sample, condition = condition, grouping = peptide, intensity = peptide_intensity_missing, ref_condition = "all", retain_columns = c(protein, peptide_intensity) ) head(data_missing, n = 24) # Perform imputation data_imputed <- impute( data_missing, sample = sample, grouping = peptide, intensity_log2 = peptide_intensity_missing, condition = condition, comparison = comparison, missingness = missingness, method = "ludovic", retain_columns = c(protein, peptide_intensity) ) head(data_imputed, n = 24)
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