filter_missval {DEP} | R Documentation |
filter_missval
filters a proteomics dataset based on missing values.
The dataset is filtered for proteins that have a maximum of
'thr' missing values in at least one condition.
filter_missval(se, thr = 0)
se |
SummarizedExperiment,
Proteomics data (output from |
thr |
Integer(1), Sets the threshold for the allowed number of missing values in at least one condition. |
A filtered 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 stringent_filter <- filter_missval(se, thr = 0) less_stringent_filter <- filter_missval(se, thr = 1)