plot_imputation {DEP} | R Documentation |
plot_imputation
generates density plots
of all conditions for input objects, e.g. before and after imputation.
plot_imputation(se, ...)
se |
SummarizedExperiment,
Data object, e.g. before imputation
(output from |
... |
Other SummarizedExperiment object(s),
E.g. data object after imputation
(output from |
Density plots of all conditions
of all conditions for input objects, e.g. before and
after imputation (generated by ggplot
).
# 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, normalize and impute missing values filt <- filter_missval(se, thr = 0) norm <- normalize_vsn(filt) imputed <- impute(norm, fun = "MinProb", q = 0.01) # Plot imputation plot_imputation(filt, norm, imputed)