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Adds new feature describing the average reporter Signal/Noise ratio.

update_average_sn.Rd

PD column Average.Reporter.SN is NA when all tags have missing values and imputes a value of zero for NA when there not all tags are missing. So, with a 10-plex TMT experiment, if a single tag has a SN of 10 and all others are NA, PD will report an average SN of 10/10 = 1.

This function adds an average reporter SN column which ignores missing values. In the example above, the average SN value reported would be 10. Where all values are NA, the average SN will remain NA.

The assumption is that the intensity values in the exprs matrix are Signal/Noise ratios, as reported by PD by default

Usage

update_average_sn(obj, sn_col = "Average.Reporter.SN")

Arguments

obj

SummarizedExperiment. Should contain PSMs-level TMT quantification

sn_col

string. Name of output column containing the average signal:noise

Value

Returns an MSnSet with the average SN included as a new feature column.