Tumor-infiltrating lymphocyte (TIL) analysis and immune microenvironment characterization using IHC markers. Specialized for immuno-oncology applications.
Usage
ihcimmune(
data,
immune_markers,
checkpoint_markers,
id = NULL,
tilAnalysis = TRUE,
tilMethod = "comprehensive",
immuneContexture = TRUE,
spatialAnalysis = FALSE,
x_coordinate,
y_coordinate,
tumorRegion,
hotspotAnalysis = FALSE,
diversityMetrics = TRUE,
checkpointScore = FALSE,
pd1Cutoff = 1,
pdl1Cutoff = 1,
cd3Threshold = 10,
cd8Threshold = 5,
immuneScoreThreshold = 10
)Arguments
- data
the data as a data frame
- immune_markers
Immune cell markers (CD3, CD4, CD8, CD20, etc.)
- checkpoint_markers
Immune checkpoint markers (PD-1, PD-L1, CTLA-4, etc.)
- id
Case identifier for tracking
- tilAnalysis
Perform specialized tumor-infiltrating lymphocyte analysis
- tilMethod
Method for TIL analysis and interpretation
- immuneContexture
Calculate immune contexture score and classification
- spatialAnalysis
Analyze spatial distribution of immune cells (requires coordinate data)
- x_coordinate
X spatial coordinates for proximity analysis
- y_coordinate
Y spatial coordinates for proximity analysis
- tumorRegion
Tumor region classification (center, invasive margin, stroma)
- hotspotAnalysis
Identify immune cell hotspots and cold regions
- diversityMetrics
Calculate Shannon and Simpson diversity indices for immune populations
- checkpointScore
Calculate composite score for checkpoint inhibitor therapy prediction
- pd1Cutoff
Threshold for PD-1 positivity assessment
- pdl1Cutoff
Threshold for PD-L1 positivity assessment
- cd3Threshold
Threshold for CD3+ TIL categorization (Low vs Intermediate)
- cd8Threshold
Threshold for CD8+ TIL categorization (Low vs Intermediate)
- immuneScoreThreshold
Threshold for overall immune infiltration categorization
Value
A results object containing:
results$instructions | a html | ||||
results$clinicalContext | a html | ||||
results$tilSummary | a table | ||||
results$immuneProfile | a table | ||||
results$checkpointAnalysis | a table | ||||
results$immuneContexture | a table | ||||
results$spatialMetrics | a table | ||||
results$hotspotAnalysis | a table | ||||
results$diversityResults | a table | ||||
results$tilMethodResults | a table | ||||
results$immunePlot | an image | ||||
results$tilPlot | an image | ||||
results$contextureHeatmap | an image | ||||
results$spatialPlot | an image | ||||
results$checkpointPlot | an image |
Tables can be converted to data frames with asDF or as.data.frame. For example:
results$tilSummary$asDF
as.data.frame(results$tilSummary)