# Immune Oncology Biological Research

## Documentation for package ‘IOBR’ version 2.2.0

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

## Help Pages

A B C D E F G H I L M N O P R S T

## -- A --

add_iobr_mirror | Add Custom Download Mirror
add_riskscore | Add Risk Score to Dataset
anno_eset | Annotate Gene Expression Matrix and Remove Duplicated Genes
assimilate_data | Harmonize Two Data Frames by Column Structure

## -- B --

batch_cor | Batch Correlation Analysis
batch_kruskal | Batch Kruskal-Wallis Test
batch_pcc | Batch Calculation of Partial Correlation Coefficients
batch_sig_surv_plot | Batch Signature Survival Plot
batch_surv | Batch Survival Analysis
batch_wilcoxon | Batch Wilcoxon Rank-Sum Test Between Two Groups
best_cutoff | Extract Best Cutoff and Add Binary Variable to Data Frame
best_cutoff2 | Extract Best Cutoff and Add Binary Variable to Data Frame
BinomialAUC | Calculate AUC for Binomial Model
BinomialModel | Binomial Model Construction

## -- C --

CalculatePref | Calculate Performance Metrics
CalculateTimeROC | Calculate Time-Dependent ROC Curve
calculate_break_month | Break Time Into Blocks
calculate_sig_score | Calculate Signature Score
calculate_sig_score_integration | Calculate Signature Score Using Integration Method
calculate_sig_score_pca | Calculate Signature Score Using PCA Method
calculate_sig_score_ssgsea | Calculate Signature Score Using ssGSEA Method
calculate_sig_score_zscore | Calculate Signature Score Using Z-Score Method
cell_bar_plot | Visualize Cell Fractions as Stacked Bar Chart
check_cancer_types | Process Batch Table and Validate Cancer Types
check_eset | Check Integrity and Outliers of Expression Set
CIBERSORT | CIBERSORT Deconvolution Algorithm
clear_iobr_cache | Clear IOBR Data Cache
combine_pd_eset | Combine Phenotype Data and Expression Set
Construct_con | Construct Contrast Matrix
ConvertRownameToLoci | Convert Rowname To Loci
CoreAlg | Core Algorithm for CIBERSORT Deconvolution
count2tpm | Convert Read Counts to Transcripts Per Million (TPM)
creat_folder | Create Nested Output Folders

## -- D --

deconvolute_quantiseq.default | Use quanTIseq to Deconvolute a Gene Expression Matrix
deconvolute_timer.default | Deconvolute Tumor Microenvironment Using TIMER
deconvo_cibersort | Deconvolve Using CIBERSORT
deconvo_epic | Deconvolve Immune Microenvironment Using EPIC
deconvo_estimate | Calculate ESTIMATE Scores
deconvo_ips | Calculate Immunophenoscore (IPS)
deconvo_mcpcounter | Deconvolve Immune Microenvironment Using MCP-Counter
deconvo_quantiseq | Deconvolve Using quanTIseq
deconvo_ref | Deconvolve Using Custom Reference
deconvo_timer | Deconvolve Using TIMER
deconvo_tme | Main TME Deconvolution Function
deconvo_xcell | Deconvolve Immune Microenvironment Using xCell
design_mytheme | Design Custom Theme for ggplot2 Plots
doPerm | Permutation Test for CIBERSORT
download_iobr_data | Download IOBR Data from GitHub with Mirror Support
DrawQQPlot | Draw QQ Plot Comparing Cancer and Immune Expression

## -- E --

Enet | Elastic Net Model Fitting
enrichment_barplot | Enrichment Bar Plot with Two Directions
EPIC | Estimate the proportion of immune and cancer cells.
eset_distribution | Visualize Expression Set Distribution
estimateScore | estimateScore
exact_pvalue | Calculate Exact P-Value for Correlation
extract_sc_data | Extract Data Frame from Seurat Object

## -- F --

feature_manipulation | Feature Quality Control and Filtering
feature_select | Feature Selection via Correlation or Differential Expression
filterCommonGenes | filterCommonGenes
find_markers_in_bulk | Identify Marker Features in Bulk Expression Data
find_mutations | Analyze Mutations Related to Signature Scores
find_outlier_samples | Identify Outlier Samples in Gene Expression Data
find_variable_genes | Identify Variable Genes in Expression Data
format_msigdb | Format Input Signatures from MSigDB
format_signatures | Transform Signature Data into List Format

## -- G --

generateRef | Generate Reference Signature Matrix
generateRef_DEseq2 | Generate Reference Signature Matrix Using DESeq2
generateRef_limma | Generate Reference Signature Matrix Using Limma
generateRef_rnaseq | Generate Reference Gene Matrix from RNA-seq DEGs
generateRef_seurat | Generate Reference Matrix from Seurat Object
GetFractions.Abbas | Constrained Regression Method (Abbas et al., 2009)
getHRandCIfromCoxph | Extract Hazard Ratio and Confidence Intervals from Cox Model
GetOutlierGenes | Get Outlier Genes
get_cols | Set and View Color Palettes
get_cor | Calculate and Visualize Correlation Between Two Variables
get_cor_matrix | Calculate and Visualize Correlation Matrix Between Two Variable Sets
get_sig_sc | Extract Top Marker Genes from Single-Cell Differential Results

## -- H --

high_var_fea | Identify High-Variance Features from Statistical Results

## -- I --

imvigor210_pdata | IMvigor210 Bladder Cancer Immunotherapy Cohort Data
iobr_cor_plot | Integrative Correlation Analysis Between Phenotype and Features
iobr_deconvo_pipeline | Tumor Microenvironment (TME) Deconvolution Pipeline
iobr_deg | Differential Expression Analysis
iobr_pca | Principal Component Analysis (PCA) Visualization
ipsmap | Map Score to Immunophenoscore
IPS_calculation | Calculate Immunophenoscore (IPS)

## -- L --

lasso_select | Feature Selection for Predictive or Prognostic Models Using LASSO Regression
limma.dif | Differential Expression Analysis Using Limma
list_github_datasets | List Available GitHub Datasets
list_iobr_mirrors | List Current Download Mirrors
load_data | Load IOBR Datasets
log2eset | Log2 Transformation of Gene Expression Matrix
LR_cal | Calculate Ligand-Receptor Interaction Scores

## -- M --

make_mut_matrix | Construct Mutation Matrices from MAF Data
mapbw | Map Score to Black and White Color
mapcolors | Map Score to Color
MCPcounter.estimate | MCP-counter Cell Population Abundance Estimation
merge_duplicate | Merge Data Frames with Duplicated Column Names
merge_eset | Merge Expression Sets by Row Names
mouse2human_eset | Convert Mouse Gene Symbols to Human Gene Symbols

## -- N --

null_models | NULL Model Coefficients for MCPcounter

## -- O --

outputGCT | outputGCT
output_sig | Save Signature Data to File

## -- P --

palettes | Select Color Palettes for Visualization
parallel_doperm | Parallel Permutation Test for CIBERSORT
ParseInputExpression | Parse Input Gene Expression Data
patterns_to_na | Default Pattern List for Name Cleaning
pdata_stad | Toy STAD Phenotype Data
percent_bar_plot | Create a Percent Bar Plot
pie_chart | Create Pie or Donut Charts
PlotAUC | Plot AUC ROC Curves
plotPurity | plotPurity
PlotTimeROC | Plot Time-Dependent ROC Curves
ProcessingData | Process Data for Model Construction
PrognosticAUC | Calculate Time-Dependent AUC for Survival Models
PrognosticModel | Build Prognostic Models Using LASSO and Ridge Regression
PrognosticResult | Compute Prognostic Results for Survival Models

## -- R --

random_strata_cells | Stratified Random Sampling of Cells
rbind_iobr | Row Bind Multiple Data Sets
RegressionResult | Regression Result Computation
RemoveBatchEffect | Remove Batch Effect of Expression Set
remove_batcheffect | Removing Batch Effect from Expression Sets
remove_duplicate_genes | Remove Duplicate Gene Symbols in Gene Expression Data
remove_names | Remove Patterns from Column Names or Variables
reset_iobr_mirrors | Reset Download Mirrors to Default
roc_time | Time-dependent ROC Curve for Survival Analysis

## -- S --

scale_matrix | Scale and Manipulate a Matrix
select_method | Select a Signature Scoring Method Subset
signature_collection | Gene signature collection for pathway and immune analysis
signature_score_calculation_methods | Signature Score Calculation Methods
sigScore | Calculate Signature Score Using PCA, Mean, or Z-score Methods
sig_box | Signature Box Plot with Statistical Comparisons
sig_box_batch | Batch Signature Box Plots for Group Comparisons
sig_forest | Forest Plot for Survival Analysis Results
sig_group | Grouped gene signatures for IOBR analysis
sig_gsea | Perform Gene Set Enrichment Analysis (GSEA)
sig_heatmap | Signature Heatmap with Optional Annotations
sig_pheatmap | Generate Heatmap for Signature Data
sig_roc | Plot ROC Curves and Compare Them
sig_surv_plot | Generate Kaplan-Meier Survival Plot for Signature
SplitTrainTest | Split Data into Training and Testing Sets
stad_group | Example Clinical Data for TCGA-STAD Gastric Cancer Analysis
subgroup_data | Example Dataset for Subgroup Survival Analysis
subgroup_survival | Subgroup Survival Analysis Using Cox Proportional Hazards Models
surv_group | Generate Kaplan-Meier Survival Plots for Categorical Groups

## -- T --

tcga_rna_preps | Preprocess TCGA RNA-seq Data
tcga_stad_pdata | TCGA-STAD Clinical and Molecular Annotation Data
test_for_infiltration | Test for Cell Population Infiltration
timer_available_cancers | TIMER Available Cancer Types
timer_info | Source code for the TIMER deconvolution method.
tme_cluster | Identification of TME Cluster
tme_deconvolution_methods | TME Deconvolution Methods
Top_probe | Top Probe Selector
transform_data | Transform NA, Inf, or Zero Values in Data