selectTopFragmentsPerPeptide: selecting top transtions WARNING - slow running function

In wolski/imsbInfer: Visualization, normalization and QC of proteomics SWATH-MS data

Description

selecting top transtions WARNING - slow running function

Usage

selectTopFragmentsPerPeptide(data, nrt = 2)

Arguments

data	- data.frame or table with at least 2 columns: transition_group_id, aggr_Fragment_Annotation (unique keys)
nrt	- top transitions to select

Examples

data(feature_alignment_requant)
table(table(feature_alignment_requant$transition_group_id))
tmp = transitions2wide(feature_alignment_requant)
# how many peptides with how many transitions
x1 = table(table(tmp$transition_group_id))
xx = selectTopFragmentsPerPeptide(tmp,nrt=7)
x2 = table(table(xx$transition_group_id))
# because with nrt 7 you do not remove any transitions
stopifnot(x1 == x2)
xx = selectTopFragmentsPerPeptide(tmp,nrt=2)
# all peptides must have 2 transitions
stopifnot(names(table(table(xx$transition_group_id))) == "2")

wolski/imsbInfer documentation built on March 27, 2021, 11:39 p.m.