retrieve_easier_score: Retrieve easier scores of immune response

In olapuentesantana/easier: Estimate Systems Immune Response from RNA-seq data

Retrieve easier scores of immune response

Description

Calculates easier score and if applicable, both weighted average and penalized score based on the combination of easier score and TMB.

Usage

retrieve_easier_score(
  predictions_immune_response = NULL,
  TMB_values = NULL,
  easier_with_TMB = c("weighted_average", "penalized_score"),
  weight_penalty,
  verbose = TRUE
)

Arguments

predictions_immune_response	list containing the predictions for each quantitative descriptor and for each task. This is the output from predict_immune_response.
TMB_values	numeric vector containing patients' tumor mutational burden (TMB) values.
easier_with_TMB	character string indicating which approach should be used to integrate easier with TMB: "weighted_average" (default) and "penalized_score".
weight_penalty	integer value from 0 to 1, which is used to define the weight or penalty for combining easier and TMB scores based on a weighted average or penalized score, in order to derive a score of patient's likelihood of immune response. The default value is 0.5.
verbose	logical flag indicating whether to display messages about the process.

Value

A data.frame with samples in rows and easier scores in columns.

Examples

# using a SummarizedExperiment object
library(SummarizedExperiment)
# Using example exemplary dataset (Mariathasan et al., Nature, 2018)
# from easierData. Original processed data is available from
# IMvigor210CoreBiologies package.
library("easierData")

dataset_mariathasan <- easierData::get_Mariathasan2018_PDL1_treatment()
RNA_tpm <- assays(dataset_mariathasan)[["tpm"]]
cancer_type <- metadata(dataset_mariathasan)[["cancertype"]]

# Select a subset of patients to reduce vignette building time.
pat_subset <- c(
  "SAM76a431ba6ce1", "SAMd3bd67996035", "SAMd3601288319e",
  "SAMba1a34b5a060", "SAM18a4dabbc557"
)
RNA_tpm <- RNA_tpm[, colnames(RNA_tpm) %in% pat_subset]

# Computation of TF activity (Garcia-Alonso et al., Genome Res, 2019)
tf_activities <- compute_TF_activity(
  RNA_tpm = RNA_tpm
)

# Predict patients' immune response
predictions <- predict_immune_response(
  tfs = tf_activities,
  cancer_type = cancer_type,
  verbose = TRUE
)

# retrieve clinical response
patient_ICBresponse <- colData(dataset_mariathasan)[["BOR"]]
names(patient_ICBresponse) <- colData(dataset_mariathasan)[["pat_id"]]

# retrieve TMB
TMB <- colData(dataset_mariathasan)[["TMB"]]
names(TMB) <- colData(dataset_mariathasan)[["pat_id"]]

patient_ICBresponse <- patient_ICBresponse[names(patient_ICBresponse) %in% pat_subset]
TMB <- TMB[names(TMB) %in% pat_subset]

easier_derived_scores <- retrieve_easier_score(
  predictions_immune_response = predictions,
  TMB_values = TMB,
  easier_with_TMB = c("weighted_average", "penalized_score"),
  weight_penalty = 0.5
)


RNA_counts <- assays(dataset_mariathasan)[["counts"]]
RNA_counts <- RNA_counts[, colnames(RNA_counts) %in% pat_subset]

# Computation of cell fractions  (Finotello et al., Genome Med, 2019)
cell_fractions <- compute_cell_fractions(RNA_tpm = RNA_tpm)

# Computation of pathway scores (Holland et al., BBAGRM, 2019;
# Schubert et al., Nat Commun, 2018)
pathway_activities <- compute_pathway_activity(
  RNA_counts = RNA_counts,
  remove_sig_genes_immune_response = TRUE
)

# Computation of ligand-receptor pair weights
lrpair_weights <- compute_LR_pairs(
  RNA_tpm = RNA_tpm,
  cancer_type = "pancan"
)

# Computation of cell-cell interaction scores
ccpair_scores <- compute_CC_pairs(
  lrpairs = lrpair_weights,
  cancer_type = "pancan"
)

# Predict patients' immune response
predictions <- predict_immune_response(
  pathways = pathway_activities,
  immunecells = cell_fractions,
  tfs = tf_activities,
  lrpairs = lrpair_weights,
  ccpairs = ccpair_scores,
  cancer_type = cancer_type,
  verbose = TRUE
)

easier_derived_scores <- retrieve_easier_score(
  predictions_immune_response = predictions,
  TMB_values = TMB,
  easier_with_TMB = c("weighted_average", "penalized_score"),
  weight_penalty = 0.5
)

olapuentesantana/easier documentation built on Feb. 25, 2024, 3:39 p.m.