Immune Oncology Biological Research

Documentation for package ‘IOBR’ version 2.2.0

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-- 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