The CASCAM class

The CASCAM class

Value

Slots

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.

sda_model

A list for the SDA model trained by the tumor data.

tumor_norm_data

A data frame of normalized tumor_aligned_data with rows for samples and columns for genes.

camod_norm_data

A data frame of normalized camod_aligned_data with rows for samples and columns for genes.

tumor_sda_project

A one column matrix showing the SDA projected vector of tumor gene expression.

camod_sda_project

A one column matrix showing the SDA projected vector of cancer model gene expression.

sda_ds

A data frame for SDA deviance score with the rows for camods and columns for tumor subtypes.

sda_lds

A data frame for SDA log deviance score with the rows for camods and columns for tumor subtypes.

sda_predict_prob

A two column matrix showing the SDA assignment probabilities for camods.

sda_ds_pval

A two column matrix showing the p-values of SDA deviance scores for camods.

sda_lds_ci

A list of two matrices showing the 95% confidence intervals of sda_lds.

genome_figure

A list of two ggplot2 figures for the genome-wide pre-selection (distribution and confidence interval).

selected_camods

The vector of genome-wide selected cancer models representing the interested tumor subtype by sda_predict_prob and sda_ds_pval.

gene_ds

A list of two matrices showing the gene-specific deviance score.

pathway_ds

A list of two matrices showing the pathway-specific deviance score.

available_pathways

A vector of available pathways.

pathway_congruence_heatmap

A ggplot2 object for the pathway congruence heatmap.

pathway_gene_heatmap

A ggplot2 object for the pathway specific heatmap.

pathway_gene_ridgeline

A ggplot2 object for the pathway specific gene expression ridgeline.

pathview_figure

A pathview figure for one specific pathway and one specific cancer model.