This function applies the qrollup method to a pepData object for each unique protein and returns a proData object.

qrollup(pepData, qrollup_thresh, combine_fn, parallel = TRUE)

Arguments

pepData

an omicsData object of class 'pepData'

qrollup_thresh

numeric value between 0 and 1 inclusive. Peptides above this threshold are used to roll up to the protein level

combine_fn

logical indicating what combine_fn to use, defaults to median, other option is mean

parallel

logical indicating whether or not to use "doParallel" loop in applying qrollup function. Defaults to TRUE.

Value

an omicsData object of class 'proData'

Details

In the qrollup method, peptides are selected according to a user selected abundance cutoff value (qrollup_thresh), and protein abundance is set as the mean of these selected peptides.

References

Polpitiya, A. D., Qian, W.-J., Jaitly, N., Petyuk, V. A., Adkins, J. N., Camp, D. G., ... Smith, R. D. (2008). DAnTE: a statistical tool for quantitative analysis of -omics data. Bioinformatics (Oxford, England), 24(13), 1556-1558.