im_syng: Find combinatorial association of immunotherapy co-targets...
In Bozorgui/imogene: : Immuno-oncology gene expression associations

Description Usage Arguments Details Value Examples

Find combinatorial association of immunotherapy co-targets with tumor intrinsic features.

im_syng(
  onco_gene,
  icp_gene,
  data_expression,
  data_feature,
  add_features,
  method,
  specificity,
  N_iteration_specificity,
  sensitivity,
  N_iteration_sensitivity
)

`onco_gene`	A character vector of gene IDs.
`icp_gene`	An optional character vector of immune checkpoint gene/protein IDs.
`data_expression`	A non-negative numeric matrix or data frame containing gene/protein expressions in linear scale.
`data_feature`	An optional numeric matrix or data frame containing immune features.
`add_features`	An optional logical indicating if EMT score, angiogenesis score and IFNG expression should be added to immune features. Default is TRUE.
`method`	A character string indicating which synergy score to be used. one of "max" or "independence". Default is "max".
`specificity`	An optional logical indicating if specificity analysis should be done. Default is FALSE.
`N_iteration_specificity`	Number of iterations for random sampling for specificity p.value calculation. Default is 1000.
`sensitivity`	An optional logical indicating if a sensitivity analysis should be done. Default is FALSE.
`N_iteration_sensitivity`	Number of iterations for random sampling for sensitivity analysis. Default is 1000.

For details of synergy score calculations see get_syng_score function.

By default (if no icp_gene is specified), icp_gene_list will be used.

data_expression is formatted with genes/proteins as rows and samples/patients as columns. For data_expression sample formats see sample_mRNA_data.

data_feature is formatted with samples/patients as rows and immune features as columns. For data_feature sample format see sample_immune_cell_fraction_data.

For synergy score calculations all features are normalized to be on 0,1 range. For details of synergy score and significance pvalue calculations see find_a_synergy function.

A specificity p.value is computed using random sampling with replacement from two null models, generated from one of the two genes against a set of genes randomly selected from the genome. Two P-values are calculated for the synergistic interaction of the pair against the two null models. The highest of the two P-values is used to assess the specificity of the interaction against the whole genome. The number of randomly selected genes in each null model is determined by N_iteration_specificity.

Sensitivity (Robustness) score defined as normalized root mean square deviation of scores calculated over 70% of samples, selected via random sampling. The number of sub-sample iterations is determined by N_iteration_sensitivity.

a data.frames of synergy scores and bootstrapping p.values

im_syng(onco_gene =  c("BRAF"),
                  icp_gene= c("CD274","CTLA4"),
                  data_expression =  sample_mRNA_data,
                  data_feature = sample_Leukocyte_fraction_data)