maxlynx2xvis: maxlynx2xvis simplify maxlynx crosslinks table for...

In heuselm/mocode: Integrates MS-based-proteomics Data Analysis Code

maxlynx2xvis simplify maxlynx crosslinks table for visualization of inter- and intra-protein crosslinks via xvis (https://xvis.genzentrum.lmu.de/CrossVisNoLogin.php)

Description

maxlynx2xvis simplify maxlynx crosslinks table for visualization of inter- and intra-protein crosslinks via xvis (https://xvis.genzentrum.lmu.de/CrossVisNoLogin.php)

Usage

maxlynx2xvis(
  combined_folder_location = "path/to/combined/",
  expDesign = NULL,
  xvis_filter = "InterProXL|IntraProXL",
  remove_decoys = TRUE,
  plot_pdf = TRUE
)

Arguments

combined_folder_location	path to combined folder location. Character, either of length 1; light crosslinker only is assumed; if two folders are provided (length 2) it is assumed that an isotopically labelled XL reagent was used; with two separate searches performed for each channel. The first folder is assumed to be from the light search and the second folder is assumed to be from the heavy search.
expDesign	In case there is no filled-in experimentalDesignTemplate.txt in the combined folder, here, a data.table with column names 'Name' and 'Experiment' should minimally be provided. Additional columns will be propagated to the output xvis_xls.csv
xvis_filter	Filter string which Crosslink types should be included in the output xvis_xls.csv; defaults to "InterProXL|IntraProXL" (both included)
plot_pdf	Logical, whether overview pdf should be generated, highlighting the ID numbers of and overlap between channels
xvis_remove_decoys	Logical, whether t-d, d-t and d-d XLs shall be removed before export to xvis_xls.csv. Defaults to TRUE.

Value

a list of 1) merged data.table of crosslinks underlying xvis_xls.csv; 2) Crosslink MSMS count table underlying summary plot; 3) Summary ggplot

heuselm/mocode documentation built on Oct. 23, 2023, 8:43 a.m.