mergePeptides {qPLEXanalyzer} | R Documentation |
Merge identical peptides to single peptide intensity. This function is especially useful for phosphopeptide analysis.
mergePeptides(MSnSetObj, summarizationFunction, annotation, keepCols = NULL)
MSnSetObj |
MSnSet; an object of class MSnSet |
summarizationFunction |
function; method used to aggregate the peptides. sum, mean or median |
annotation |
data.frame; a data.frame of protein annotation of four columns: "Accessions", "Gene", "Description" and "GeneSymbol" |
keepCols |
a vector of additional columns from fData(MSnSetObj) to keep. either be a numeric vector of column indices or a character vector of column names |
Rows of the intensity matrix with identical peptide sequences are merged by
summarising the intensities using summarizationFunction
.
Columns specified with keepCols
are retained in the final output.
Non-unique entries in different rows are concatenated with ';'.
An object of class MSnSet
(see MSnSet-class
)
data(human_anno) data(exp3_OHT_ESR1) MSnSet_data <- convertToMSnset(exp3_OHT_ESR1$intensities_qPLEX1, metadata=exp3_OHT_ESR1$metadata_qPLEX1, indExpData=c(7:16), Sequences=2, Accessions=6) MSnset_P <- mergePeptides(MSnSet_data, sum, human_anno)