ppi.analyze: BS3 Differential Analysis Inclusive Function

Description Usage Arguments

View source: R/pdb_functions2.R

Description

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

Usage

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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)

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 Sept. 8, 2018, 9:30 p.m.