ppi.analyze: BS3 Differential Analysis Inclusive Function

In egmg726/crisscrosslinker: An R package for protein interaction analysis

Description

This function combines many of the features of the BS3 XL-MS workflow for ease of use

Usage

ppi.analyze(
  list_of_files,
  fasta_file,
  file_type_2d = c("single_dot", "linear", "curved"),
  fasta_names_to_generate_all_2d_structures = NULL,
  csv_pdb_input_file = NULL,
  category_color_input_file = NULL,
  show_only_real_structures = NULL,
  distance_histogram_name = "distance_histogram.png",
  pymol_file_list_file_name = "pymol_ts_output.pml",
  xlink_df_name = "xlink_dataframe.csv",
  xlink_view_file_name = "xlink_view_df.csv",
  no_pdb_files = FALSE,
  protein_alternative_names_dict = NULL,
  pdb_directory = NULL,
  data_input_type = "plink",
  pdb_numbering = FALSE,
  pdb_match_vector = NULL
)

Arguments

list_of_files	A list of file names containing pLink data to be used for the analysis
fasta_file	FASTA file as loaded by seqinr::read.fasta()
file_type_2d	The type of file used for PDB creation. "single_dot" creates PDB files with peptides represented by single dots.
fasta_names_to_generate_all_2d_structures	List of protein names corresponding to names in FASTA file to automatically make into 2D PDB structures. Defaults to NULL.
csv_pdb_input_file	csv_pdb_input_file
category_color_input_file	category_color_input_file
show_only_real_structures	show_only_real_structures
distance_histogram_name	distance_histogram_name
pymol_file_list_file_name	pymol_file_list_file_name
xlink_df_name	xlink_df_name
xlink_view_file_name	xlink_view_file_name
no_pdb_files	no_pdb_files
protein_alternative_names_dict	protein_alternative_names_dict
pdb_directory	pdb_directory
data_input_type	data_input_type

egmg726/crisscrosslinker documentation built on Jan. 23, 2021, 1:50 a.m.