tcga.cn.convert

A matrix of DNA copy number data included in the GISTIC2 output. Typically all_data_by_genes.txt, or a subset thereof,
including the Locus.ID and Cytoband columns.

cn.mat

This function reformats DNA copy number matrices obtained from the Broad Institute's Firehose GDAC 
 (<a href="https://gdac.broadinstitute.org/">https://gdac.broadinstitute.org/</a>) so they can be used as input for mVisAGe functions.

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>.

Vonn Walter

MVisAGe

Compute and Visualize Bivariate Associations

tcga.cn.convert function

This function reformats DNA copy number matrices obtained from the Broad Institute's Firehose GDAC 
 (<a href='https://gdac.broadinstitute.org/'>https://gdac.broadinstitute.org/</a>) so they can be used as input for mVisAGe functions.

tcga.cn.convert: A Function for Reformatting TCGA DNA Copy Number Matrices

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Examples