msarc.subtract: Subtract Control From Experiment
In msarc: Draw Diagrams (mis)Representing the Results of Mass Spec Experiments

Description Usage Arguments Details Value Author(s) Examples

Removes Uniprot IDs from an msarc object if they also occur in a "control" object (or a simple vector of Uniprot IDs).

1	msarc.subtract(source, control)

`source`	the `msarc` object of interest
`control`	the background control, either another `msarc` object, or a simple vector of Uniprot IDs

Typically this will be used to remove “background” proteins, such as those obtained from an IgG control, from an experiment, to reveal those proteins which are specific to the experiment of interest. Customarily, a mass spec experiment will include a treated sample of some sort, and a corresponding untreated sample. The peptides that are identified only in the treated sample are taken to be the interesting ones. This function allows the straightforward removal from the treatment object of proteins that also occur in the untreated control.

the modified source msarc object.

Gord Brown

# Load a data set and control
data('sample_initial',package="msarc")
data('control_initial',package="msarc")
sample_subtracted <- msarc.subtract(sample_initial,control_initial)