Description
Compute and Visualize Bivariate Associations.
Description
Pearson and Spearman correlation coefficients are commonly used to quantify the strength of bivariate associations of genomic variables. For example, correlations of gene-level DNA copy number and gene expression measurements may be used to assess the impact of DNA copy number changes on gene expression in tumor tissue. 'MVisAGe' enables users to quickly compute and visualize the correlations in order to assess the effect of regional genomic events such as changes in DNA copy number or DNA methylation level. Please see Walter V, Du Y, Danilova L, Hayward MC, Hayes DN, 2018. Cancer Research <doi:10.1158/0008-5472.CAN-17-3464>.
README.md
MVisAGe
DNA copy number changes (gains and losses) are commonly seen in tumor tissue. Although these events occur randomly throughout the genome, some provide a selective growth advantage because they lead to increased (gains) or decreased (losses) expression of affected genes. MVisAGe was designed to help users explore the effects of copy number changes and alterations in DNA methylation status on gene expression. Gene-level Pearson and Spearman correlation coefficients are computed and plotted according to the genomic position of the underlying genes.
Example
Please refer to the vignette.