manual_impute {DEP} | R Documentation |
manual_impute
imputes missing values in a proteomics dataset
by random draws from a manually defined distribution.
manual_impute(se, scale = 0.3, shift = 1.8)
se |
SummarizedExperiment,
Proteomics data (output from |
scale |
Numeric(1), Sets the width of the distribution relative to the standard deviation of the original distribution. |
shift |
Numeric(1), Sets the left-shift of the distribution (in standard deviations) from the median of the original distribution. |
An imputed SummarizedExperiment object.
# Load example data <- UbiLength data <- data[data$Reverse != "+" & data$Potential.contaminant != "+",] data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";") # Make SummarizedExperiment columns <- grep("LFQ.", colnames(data_unique)) exp_design <- UbiLength_ExpDesign se <- make_se(data_unique, columns, exp_design) # Filter and normalize filt <- filter_missval(se, thr = 0) norm <- normalize_vsn(filt) # Impute missing values manually imputed_manual <- impute(norm, fun = "man", shift = 1.8, scale = 0.3)