Bloodgen3module

BloodGen3Module

Workflows

Standard Workflow

library(BloodGen3Module)
library(ExperimentHub)
library(SummarizedExperiment)

# 1. Load expression data from ExperimentHub
dat <- ExperimentHub()
res <- query(dat, "GSE13015")
GSE13015 <- res[["EH5429"]]

# 2. Perform group comparison analysis using t-test
Group_df <- Groupcomparison(
  GSE13015,
  sample_info = NULL,
  FC = 1.5,
  pval = 0.1,
  FDR = TRUE,
  Group_column = "Group_test",
  Test_group = "Sepsis",
  Ref_group = "Control",
  SummarizedExperiment = TRUE
)

# 3. Perform group comparison analysis using limma
Group_limma <- Groupcomparisonlimma(
  GSE13015,
  sample_info = NULL,
  FC = 1.5,
  pval = 0.1,
  FDR = TRUE,
  Group_column = "Group_test",
  Test_group = "Sepsis",
  Ref_group = "Control",
  SummarizedExperiment = TRUE
)

# 4. Generate fingerprint grid plot
gridplot(
  Group_df,
  cutoff = 15,
  Ref_group = "Control",
  filename = tempfile()
)

# 5. Perform individual single sample analysis
Individual_df <- Individualcomparison(
  GSE13015,
  sample_info = NULL,
  FC = 1.5,
  DIFF = 10,
  Group_column = "Group_test",
  Ref_group = "Control",
  SummarizedExperiment = TRUE
)

# 6. Generate individual fingerprint heatmap
fingerprintplot(
  Individual_df,
  sample_info = NULL,
  cutoff = 15,
  rowSplit = TRUE,
  Group_column = "Group_test",
  show_ref_group = FALSE,
  Ref_group = "Control",
  Aggregate = "A28",
  filename = tempfile(),
  height = NULL,
  width = NULL
)

Input/Output Note: Inputs a SummarizedExperiment or expression matrix with sample annotations; outputs data frames of module-level percentages and generates PDF visualizations of fingerprint grids and heatmaps.

When to Use

• To perform blood transcriptional module repertoire analysis on gene expression data.
• To determine the percentage of constitutive genes for each module that are significantly increased or decreased between groups using Groupcomparison() or Groupcomparisonlimma().
• To perform individual sample-level modular analysis in reference to a control group using Individualcomparison().
• To visualize group comparison results as a fingerprint grid using gridplot() or individual comparisons as a fingerprint heatmap using fingerprintplot().

When NOT to Use

• For general-purpose differential gene expression analysis without modular grouping (use limma or DESeq2 directly).
• For single-cell RNA-seq data requiring cell-type specific clustering and marker identification (use Seurat or scran instead).

Data Requirements

• A normalized, non-log2-transformed expression data matrix or a SummarizedExperiment object (log2 transformation is performed automatically).
• A sample annotation table (if not using a SummarizedExperiment with built-in colData) where the row names match the column names of the expression matrix.

Key Parameters

• FC (1.5): Fold change threshold for determining significant changes in gene expression.
• pval (0.1): P-value threshold for statistical significance.
• FDR (TRUE): Logical indicating whether to apply False Discovery Rate correction.
• Group_column ("Group_test"): Column name in sample metadata containing the group classifications.
• Test_group ("Sepsis"): Name of the group to be tested.
• Ref_group ("Control"): Name of the reference group.
• SummarizedExperiment (TRUE): Logical indicating if the input is a SummarizedExperiment object.
• cutoff (15): Percentage threshold for module visualization in grid and fingerprint plots.

Best Practices

• Ensure the input expression matrix is not log2-transformed, as the package functions perform log2 transformation internally.
• Verify that the row names of the sample information table (sample_info) match the column names of the expression matrix exactly.
• Use Groupcomparisonlimma() instead of Groupcomparison() when dealing with complex experimental designs or when limma's empirical Bayes moderation is preferred.

Common Pitfalls

• Pitfall: Inputting pre-log-transformed data, leading to incorrect fold change calculations. Fix: Provide raw or normalized linear-scale counts/intensities.
• Pitfall: Mismatched sample names between expression matrix columns and annotation row names. Fix: Align the names using colnames(data) <- rownames(sample_info) before running the analysis.

Alternatives

• tmod for general gene set enrichment and module visualization.
• GSVA for gene set variation analysis.
• clusterProfiler for standard GO/KEGG functional enrichment.

Citations

• Rinchai D, et al. (2021). "BloodGen3Module: blood transcriptional module repertoire analysis and visualization using R." Bioinformatics. doi:10.1093/bioinformatics/btab121.

References

• Homepage: https://bioconductor.org/packages/bloodgen3module
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/bloodgen3module/inst/doc/BloodGen3Module.html