create_mdata: Create feature metadata
In evanamartin/TopPICR: What the Package Does (One Line, Title Case)

create_mdata

R Documentation

Create feature metadata

Description

This function uses the information from the identified feature data to create a feature metadata data frame. This data frame will be used at the end of the TopPICR pipeline when creating an MSnSet object.

Usage

create_mdata(x, errors, n_mme_sd, n_rt_sd)

Arguments

`x`	A `data.table` output from the `create_pcg` function.
`errors`	A `list` output from the `calc_error` function. The first element of the list contains the standard deviation and median of the mass measurement error for each data set. The second element is the standard deviation of the mass measurement error across all data sets. The third element is the standard deviation of the retention time in seconds across all data sets.
`n_mme_sd`	A numeric value indicating the number of standard deviations in ppm. This value is used as the threshold for determining if two clusters (from two different genes) have the same centroid in mass space.
`n_rt_sd`	A numeric value representing the number of standard deviations in seconds. This value is used as the threshold for determining if two clusters (from two different genes) have the same centroid in retention time space.

Value

A data.table with a row for each unique combination of Gene, pcGroup, and Proteoform. The collision variable indicates which clusters have the same centroid across different genes. The data.table also contains other proteoform information such as protein length, UniProt accession, and first and last amino acid among others.