Source: https://github.com/aipoch/medical-research-skills
ssGSEA Immune Infiltration Analysis
When to Use
- Estimate relative immune infiltration from a bulk RNA-seq expression matrix.
- Compare immune enrichment scores between one case group and one control group.
- Generate structured result tables plus optional PDF visualizations for downstream review.
When Not to Use
- Single-cell RNA-seq or spatial transcriptomics.
- Absolute immune cell proportion estimation or deconvolution.
- Clinical diagnosis, treatment recommendation, or any other medical decision making.
Workflow
- Confirm that the expression matrix, group file, and gene-set file match the documented schemas.
- Run
scripts/main.R with the target case and control groups.
- Review
run_record.txt, output_manifest.txt, and the generated tables or plots.
- If execution fails, read
references/troubleshooting.md before retrying.
When to Read External Files
| Situation | File to Read | Purpose |
|---|
| Need to run the analysis | scripts/main.R | CLI entry point |
| Need algorithm details | references/algorithm.md | Method assumptions and interpretation |
| Encounter an error | references/troubleshooting.md | Error codes and fixes |
| Need CLI examples or baseline execution details | references/cli-guide.md | Examples and recorded run details |
| Need dependency declarations | DESCRIPTION | Package list and Bioconductor source note |
| Need test commands | tests/run_tests.R | End-to-end test entry |
Usage
Rscript scripts/main.R \
--input_file ./expression_matrix.csv \
--group_file ./group_info.csv \
--gene_set ./immune_gene_sets.csv \
--case_group treatment \
--control_group control \
--output_dir ./output \
--method ssgsea \
--seed 42
Validated path note:
ssgsea is the default validated path.gsva is supported, but only with kernels validated in the local GSVA environment.- In the current audited environment,
gsva with Gaussian completed successfully and is the documented baseline.
Arguments
| Short | Long | Type | Default | Description |
|---|
-i | --input_file | file | required | Expression matrix with genes as rows and samples as columns |
-g | --group_file | file | required | Group annotation table |
-e | --gene_set | file | tests/data/immune_gene_sets.csv | Immune gene-set CSV |
-a | --case_group | string | required | Case group label |
-b | --control_group | string | required | Control group label |
-o | --output_dir | dir | ./output | Output directory |
-m | --method | string | ssgsea | GSVA method: ssgsea, gsva |
-k | --kcdf | string | Gaussian | Kernel mode: Gaussian, Poisson; Gaussian is the validated GSVA baseline |
-n | --min_sz | integer | 2 | Minimum overlap genes per gene set |
-x | --max_sz | integer | 10000 | Maximum genes per gene set |
-p | --parallel_sz | integer | 2 | Requested parallel CPU count |
-u | --tau | numeric | 0.25 | Tau parameter for ssGSEA |
-d | --mx_diff | boolean | true | GSVA mx.diff switch |
-c | --gene_id_case | string | upper | Gene ID normalization: asis, upper, lower |
-s | --seed | integer | 42 | Random seed |
-t | --timeout_seconds | integer | 0 | Optional timeout; 0 disables it |
| --sample_col | string/int | none | Sample column name or 1-based index |
| --group_col | string/int | none | Group column name or 1-based index |
| --make_plots | boolean | true | Generate PDF plots |
| --verbose | boolean | true | Print progress logs |
Input Format
Expression Matrix
CSV or TSV. The first column must contain gene identifiers. Remaining columns are sample-level numeric expression values.
gene,Sample1,Sample2,Sample3
TP53,10.2,8.5,9.1
CXCL9,4.3,6.1,5.7
Group File
CSV or TSV with at least one sample column and one group column.
sample,group
Sample1,control
Sample2,treatment
Sample3,treatment
Gene Set File
CSV with gene and cell_type; immunity_class is optional.
gene,cell_type,immunity_class
CXCL9,Activated CD8 T cell,Adaptive
CD3D,Activated CD8 T cell,Adaptive
Output Files
| File | Description |
|---|
data/ssgsea_list.rds | Serialized analysis result object |
table/ssgsea_scores_long.csv | Long-format immune infiltration scores |
table/ssgsea_scores_wide.csv | Wide-format immune infiltration score matrix |
table/ssgsea_group_compare.csv | Case-vs-control comparison summary |
table/immune_cell_correlation_matrix.csv | Immune-cell Spearman correlation matrix |
table/immune_cell_correlation_pvalue.csv | Correlation p-value matrix |
plot/immune_cell_composition_sample.pdf | Sample-level composition plot; generated only when --make_plots=true |
plot/immune_group_boxplot.pdf | Group comparison boxplot; generated only when --make_plots=true |
plot/immune_correlation_heatmap.pdf | Immune-cell correlation heatmap; generated only when --make_plots=true |
plot/gene_immune_correlation_scatter_*.pdf | Auto-selected gene-vs-cell scatter plot; generated only when --make_plots=true |
run_record.txt | Structured execution record |
output_manifest.txt | Output file manifest with descriptions |
session_info.txt | R session information |
Error Handling
| Error | Cause | Solution |
|---|
SKILL_FILE_NOT_FOUND | Input file path is invalid | Check file paths |
SKILL_MISSING_COLUMNS | Required columns are absent | Fix the input schema |
SKILL_EMPTY_DATA | No usable rows, gene sets, or aligned samples remain | Check IDs and filters |
SKILL_INVALID_PARAMETER | CLI value is invalid or data is malformed | Review arguments and file content |
SKILL_SAMPLE_MISMATCH | Expression and group samples do not align | Harmonize sample identifiers |
SKILL_PACKAGE_NOT_FOUND | Required R package is missing | Install the missing package |
SKILL_TIMEOUT | The configured time limit was exceeded | Increase --timeout_seconds or disable it with 0 |
Testing
Rscript scripts/main.R --help
Rscript tests/run_tests.R
Rscript tests/test_skill.R
tests/test_skill.R is self-contained: if expected outputs are absent, it first runs tests/run_tests.R and then validates both file presence and core result structure.