This function evaluates the variability within all protein group
MSnSet. If a protein group is composed only of a
NA is returned.
aggvar(object, groupBy, fun)
An object of class
A function the summarise the distance between features
within protein groups, typically
matrix providing the number of features per
protein group (
nb_feats column) and the aggregation
summarising distance (
This function can be used to identify protein groups with
incoherent feature (petides or PSMs) expression patterns. Using
max as a function, one can identify protein groups with
single extreme outliers, such as, for example, a mis-identified
peptide that was erroneously assigned to that protein group. Using
mean identifies more systematic inconsistencies where, for
example, the subsets of peptide (or PSM) feautres correspond to
proteins with different expression patterns.
combineFeatures to combine PSMs
quantitation into peptides and/or into proteins.
library("pRolocdata") data(hyperLOPIT2015ms3r1psm) groupBy <- "Protein.Group.Accessions" res1 <- aggvar(hyperLOPIT2015ms3r1psm, groupBy, fun = max) res2 <- aggvar(hyperLOPIT2015ms3r1psm, groupBy, fun = mean) par(mfrow = c(1, 3)) plot(res1, log = "y", main = "Single outliers (max)") plot(res2, log = "y", main = "Overall inconsistency (mean)") plot(res1[, "agg_dist"], res2[, "agg_dist"], xlab = "max", ylab = "mean")