plot_missval {DEP} | R Documentation |
plot_missval
generates a heatmap of proteins
with missing values to discover whether values are missing by random or not.
plot_missval(se)
se |
SummarizedExperiment, Data object with missing values. |
A heatmap indicating whether values are missing (0) or not (1)
(generated by Heatmap
).
# 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) # Plot missing values heatmap plot_missval(filt)