im_cor: Calculate Spearman correlation with immune checkpoints
In Bozorgui/imogene: : Immuno-oncology gene expression associations

Description Usage Arguments Details Value Examples

Calculate Spearman correlation with immune checkpoints

1	im_cor(onco_gene, icp_gene, data_expression, data_feature, add_features)

`onco_gene`	A character vector of gene/protein IDs.
`icp_gene`	An optional character vector of immune checkpoint gene/protein IDs.
`data_expression`	A numeric matrix or data frame containing gene/protein expressions.
`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.

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 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_Leukocyte_fraction_data.

A list of dataframes containing Spearman correlations and non-FDR adjusted probability values.

im_cor(onco_gene =  c("BRAF","CTLA4"),
                 icp_gene= c("CD274","CTLA4"),
                 data_expression =  sample_mRNA_data,
                 data_feature = sample_immune_cell_fraction_data,
                 add_features=TRUE)