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Calculate Ligand-Receptor Interaction Scores

Source: R/LR_cal.R
LR_cal.Rd

Quantifies ligand-receptor interactions in the tumor microenvironment from bulk gene expression data using the easier package. This function processes raw counts or TPM data and computes interaction scores for each sample.

Usage

LR_cal(
  eset,
  data_type = c("count", "tpm"),
  id_type = "ensembl",
  cancer_type = "pancan"
)

Arguments

eset

Gene expression matrix with genes as rows and samples as columns.

data_type

Type of input data. Options are `"count"` or `"tpm"`. If `"count"`, data will be converted to TPM before analysis.

id_type

Type of gene identifier. Default is `"ensembl"`.

cancer_type

Character string specifying the cancer type for easier. Default is `"pancan"` for pan-cancer analysis.

Value

Data frame containing ligand-receptor interaction scores with sample IDs as row names.

References

Lapuente-Santana, van Genderen, M., Hilbers, P., Finotello, F., & Eduati, F. (2021). Interpretable systems biomarkers predict response to immune-checkpoint inhibitors. Patterns (New York, N.Y.), 2(8), 100293. https://doi.org/10.1016/j.patter.2021.100293

Examples

# LR_cal requires HGNC gene symbols as rownames
# Create a simple example with gene symbols
example_genes <- c(
  "TGFB1", "EGFR", "VEGFA", "PDGFB", "FGF2", "CXCL12",
  "CXCR4", "IL6", "IL6R", "TNF", "TNFRSF1A", "IFNG"
)
sim_eset <- as.data.frame(matrix(
  rnorm(length(example_genes) * 10, mean = 5, sd = 2),
  nrow = length(example_genes), ncol = 10
))
rownames(sim_eset) <- example_genes
colnames(sim_eset) <- paste0("Sample", 1:10)
# \donttest{
if (requireNamespace("easier", quietly = TRUE)) {
  lr <- LR_cal(eset = sim_eset, data_type = "tpm")
  head(lr)
}
#> Warning: replacing previous import ‘S4Arrays::makeNindexFromArrayViewport’ by ‘DelayedArray::makeNindexFromArrayViewport’ when loading ‘SummarizedExperiment’
#> 
#> 
#> 
#> LR signature genes found in data set: 11/644 (1.7%)
#> Ligand-Receptor pair weights computed 
#>        ID CXCL12_CXCR4   IL6_IL6R TNF_TNFRSF1A_TNFRSF21_TRAF2
#> 1 Sample1     2.368152  2.4361612                    2.341010
#> 2 Sample2     2.759510 -0.2755479                    1.052273
#> 3 Sample3     2.057308  2.7174774                    2.716119
#> 4 Sample4     2.426236  2.1919763                    2.178430
#> 5 Sample5     2.328362  2.6795345                    1.777969
#> 6 Sample6     2.582983  2.5136527                    2.255756
# }