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Predict Niche Protein-Protein Interactions

Source: R/SingleSampAnalysis.R
CalSampPPI.Rd

Predicts pathogen-host protein-protein interactions using BLAST homology search and STRING database integration. Constructs and visualizes PPI networks.

Usage

CalSampPPI(
  STID_obj = NULL,
  p.fasta_path = NULL,
  h.fasta_path = NULL,
  p.symbol2protein_path = NULL,
  h.symbol2protein_path = NULL,
  p.features = NULL,
  h.features = NULL,
  BLAST_tool = "blastp",
  dbtype = "prot",
  BLAST_args = "-evalue 1e-10 -max_target_seqs 5 -max_hsps 50 -num_threads 4",
  BLAST_fil_args = "pident > 40, evalue < 1e-10, bitscore > 100, length > 100",
  version_STRING = "12.0",
  score_thre_only = 100,
  score_thre_all = 700,
  return_data = TRUE,
  grp_nm = NULL,
  dir_nm = "M3_CalSampPPI"
)

Arguments

STID_obj

An STID object containing niche analysis results

p.fasta_path

Character, path to pathogen protein FASTA file

h.fasta_path

Character, path to host protein FASTA file

p.symbol2protein_path

Character, pathogen gene symbol to protein ID mapping file

h.symbol2protein_path

Character, host gene symbol to protein ID mapping file

p.features

Character vector, pathogen genes to include

h.features

Character vector, host genes to include

BLAST_tool

Character, BLAST tool to use (default: "blastp")

dbtype

Character, database type (default: "prot")

BLAST_args

Character, BLAST search arguments (default: "-evalue 1e-10 -max_target_seqs 5 -max_hsps 50 -num_threads 4")

BLAST_fil_args

Character, BLAST result filtering criteria

version_STRING

Character, STRING database version (default: "12.0")

score_thre_only

Numeric, score threshold for pathogen-only network (default: 100)

score_thre_all

Numeric, score threshold for full network (default: 700)

return_data

Logical, whether to return results list (default: TRUE)

grp_nm

Character, group name for output organization (default: NULL)

dir_nm

Character, directory name for output (default: "M3_CalSampPPI")

Value

If return_data = TRUE, returns a list of PPI results

Examples

if (FALSE) { # \dontrun{
# Predict pathogen-host PPIs
results <- CalSampPPI(
  STID_obj = STID_obj,
  p.fasta_path = "pathogen_proteins.fasta",
  h.fasta_path = "host_proteins.fasta",
  p.symbol2protein_path = "pathogen_mapping.txt",
  h.symbol2protein_path = "host_mapping.txt"
)
} # }