dissect_TDsummary: Dissect a TDSummary file

In davidsbutcher/viztools: Innovative visualizations for top-down proteomics

Description

Extracts data from sheets in a top-down summary file and formats it for use in making an UpSet plot with UpSet_maker() or intersection degree plot with make_intersect_plot() . Searches for a sheet in the TDsummary named according to the arguments shortName and proteinSheetName, pformSheetName, or unfracSheetName in the form "shortName_sheetName", e.g. "peppi04d_fractions_protein". This function is included for use in the package author's workflow and may not be useful for others.

Usage

dissect_TDsummary(
  TDsummarypath,
  shortName = NULL,
  UpSetType = "protein",
  proteinSheetName = "fractions_protein",
  pformSheetName = "fractions_proteoform",
  unfracSheetName = "runs_protein"
)

Arguments

TDsummarypath	Full path to TDsummary file. Should be .xlsx format.
shortName	Analysis shortnames to use to make UpSets.
UpSetType	Type of UpSet plot to make - "protein", "proteoform", or "protein_unfrac"

Value

A list of UniProt accessions or proteoform record numbers properly formatted for use with the UpSet_maker() function.

Examples

## Not run: 
dissect_TDsummary(
   "C:/Users/Bakunin/Documents/TDdatasummary.xlsx",
   c("peppi04d"),
   UpSetType = "protein"
)

## End(Not run)

davidsbutcher/viztools documentation built on Oct. 5, 2020, 3:25 a.m.