cn.mat

Quantitative gene-level DNA copy number measurements for 98 samples from The
Cancer Genome Atlas (TCGA) HNSC cohort. The all_data_by_genes.txt dataset from
the GISTIC2 output was restricted to the first 100 columns and genes that lie
on chromosomes 11 and 12. Genes appear in rows; samples appear in columns (other
than the first two columns described below). Gene symbols are used as row
names and sample identifiers are used as column names (other than the first two columns).

datasets

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

cn.mat function

A matrix with 2719 rows and 100 columns<dl class="dl-horizontal">
<dt>Locus.ID</dt><dd>gene identifier</dd>
<dt>Cytoband</dt><dd>cytoband containing the gene of interest</dd>
<dt>Remaining Columns</dt><dd>quantitative DNA copy number</dd>
<dt>Column names</dt><dd>sample identifiers (other than the first two columns)</dd>
<dt>Row names</dt><dd>gene symbols</dd>
</dl>

Format

DNA copy number data from 98 head and neck squamous cell carcinoma (HNSC) patients — cn.mat

A matrix with 2719 rows and 100 columns<dl class='dl-horizontal'>
<dt>Locus.ID</dt><dd>gene identifier</dd>
<dt>Cytoband</dt><dd>cytoband containing the gene of interest</dd>
<dt>Remaining Columns</dt><dd>quantitative DNA copy number</dd>
<dt>Column names</dt><dd>sample identifiers (other than the first two columns)</dd>
<dt>Row names</dt><dd>gene symbols</dd>
</dl>

cn.mat: DNA copy number data from 98 head and neck squamous cell carcinoma (HNSC) patients

Description

Usage

Arguments

Format