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Create a CASCAM object

create_CASCAM.Rd

This function creates a CASCAM object for the downstream analysis. The data sets of tumor aligned gene expression data with the tumor subtype labels and cancer model aligned gene expression data are needed as the input. Celligner is highly recommended to align the tumor and cancer model data.

Usage

create_CASCAM(tumor_aligned_data, tumor_label, camod_aligned_data, info_object)

Arguments

tumor_aligned_data

A data frame of aligned tumor gene expression with rows for genes and columns for samples.

tumor_label

A vector of strings indicating the labels of the tumor samples.

camod_aligned_data

A data.frame of aligned cancer model gene expression with rows for genes and columns for samples.

info_object

An InformativeGenes object for the study.

Value

A CASCAM object.

Examples

if (FALSE) {
gene_info <- create_InformativeGenes(tumor_ct, tumor_label2, "ILC")
CASCAM_eg <- create_CASCAM(tumor_aligned, tumor_label, camod_aligned, gene_info)
}