# Host-Pathogen Interaction Prediction

## Documentation for package ‘HPiP’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

calculateAAC | Calculate Amino Acid Composition (AAC) Descriptor
calculateAutocor | Calculate Autocorrelation Descriptors
calculateBE | Tranform a Seqeuence into Binary Encoding (BE)
calculateCTDC | Calculate CTD Descriptors - Composition (C)
calculateCTDD | Calculate CTD Descriptors - Distribution (D)
calculateCTDT | Calculate CTD Descriptors - Transition (T)
calculateCTriad | Calculate Conjoint Triad Descriptor
calculateDC | Calculate Dipeptide Composition (DC) Descriptor
calculateF | Calculate F1 or F2 Descriptors
calculateKSAAP | Calculate k-spaced Amino Acid Pairs (KSAAP) Descriptor
calculateQD_Sm | Calculate Quadruples Composition (QC) Descriptor from Biochemical Similarity Classes
calculateTC | Calculate Tripeptide Composition (TC) Descriptor
calculateTC_Sm | Calculate Tripeptide Composition (TC) Descriptor from Biochemical Similarity Classes
corr_plot | Plot Correlation Matrix between Input Features
enrich.df | Enrichment Result
enrichfindP | Functional Enrichment Analysis for Pathogen Interactors in the High-Confidence Network.
enrichfind_cpx | Functional Enrichment Analysis for Predicted Modules
enrichfind_hp | Functional Enrichment Analysis of all Host Proteins
enrichplot | Plot the Enrichment Reuslt
example_data | Input Data for Prediction Algorithm
filter_missing_values | Drop the Missing Values Above a Certain Threshold
FreqInteractors | Plot the Pathogen Proteins' frequency of Interactions with Host Proteins
FSmethod | Feature Selection via Matrix Correlation and Recursive Feature Elimination (RFE)
getFASTA | Fetch FASTA Sequence from the UniProt Database
getHPI | Generating Host-Pathogen Protein-Protein Interaction (HP-PPI) Descriptors
get_negativePPI | Construct Negative Reference Host-Pathogen Protein-Protein Interactions (HP-PPIs)
get_positivePPI | Fetch Positive Reference Host-Pathogen Protein-Protein Interactions (HP-PPIs) from the BioGRID Database
Gold_ReferenceSet | Gold-standard Reference Set of Inter-Species PPIs
host_se | Host SummarizedExperiment object
impute_missing_data | Impute missing Values per Features (i.e., Columns)
plotPPI | Plot the Predicted PPI
predicted_PPIs | Predicted HP-PPIs
pred_ensembel | Predict Interactions via Ensemble Learning Method
run_clustering | Module Detection
unlabel_data | HP-PPIs with Unknown Class Labels
UP000464024_df | Data.frame Containing SARS-CoV-2 FASTA Sequences
var_imp | Variable Importance Plot
viral_se | Viral SummarizedExperiment object