mergeSites: Merge identical modification sites intensities

In crukci-bioinformatics/qPLEXanalyzer: Tools for quantitative proteomics data analysis

Merge identical modification sites intensities

Description

Merge peptides with identical modification sites to single site intensity. This function is especially useful for data based on enrichment of specific peptide modification.

Usage

mergeSites(MSnSetObj, summarizationFunction, annotation, keepCols = NULL)

Arguments

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

Details

Rows of the intensity matrix with identical sites on same protein are merged by summarising the intensities using summarizationFunction. The merging will only take place if "Sites" and "Type" column are present in the fData(MSnSetObj). Sites contains the information of modified site position within the protein sequence and Type tells us about whether the modification is single (1xPhospho/Acetyl) or multi (2xPhospho/Acetyl).

Columns specified with keepCols are retained in the final output. Non-unique entries in different rows are concatenated with ';'.

Value

An object of class MSnSet (see MSnSet-class)

Examples

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 <- mergeSites(MSnSet_data, sum, human_anno)

crukci-bioinformatics/qPLEXanalyzer documentation built on Sept. 24, 2024, 1:13 a.m.