gdcCorPlot: Correlation plot of two genes/miRNAs

Description Usage Arguments Value Author(s) Examples

View source: R/gdcCorPlot.R

Description

Scatter plot showing the expression correlation between two genes/miRNAs

Usage

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gdcCorPlot(gene1, gene2, rna.expr, metadata)

Arguments

gene1

an Ensembl gene id or miRBase v21 mature miRNA id

gene2

an Ensembl gene id or miRBase v21 mature miRNA id

rna.expr

voom transformed expression data

metadata

metadata parsed from gdcParseMetadata

Value

A scatter plot with line of best fit

Author(s)

Ruidong Li and Han Qu

Examples

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genes <- c('ENSG00000000938','ENSG00000000971','ENSG00000001036',
        'ENSG00000001084','ENSG00000001167','ENSG00000001460')

samples <- c('TCGA-2F-A9KO-01', 'TCGA-2F-A9KP-01', 
            'TCGA-2F-A9KQ-01', 'TCGA-2F-A9KR-11', 
            'TCGA-2F-A9KT-11', 'TCGA-2F-A9KW-11')
             
metaMatrix <- data.frame(sample_type=rep(c('PrimaryTumor',
                        'SolidTissueNormal'),each=3),
                        sample=samples,
                        days_to_death=seq(100,600,100),
                        days_to_last_follow_up=rep(NA,6))

rnaExpr <- matrix(c(2.7,7.0,4.9,6.9,4.6,2.5,
                    0.5,2.5,5.7,6.5,4.9,3.8,
                    2.1,2.9,5.9,5.7,4.5,3.5,
                    2.7,5.9,4.5,5.8,5.2,3.0,
                    2.5,2.2,5.3,4.4,4.4,2.9,
                    2.4,3.8,6.2,3.8,3.8,4.2),6,6)
rownames(rnaExpr) <- genes
colnames(rnaExpr) <- samples
gdcCorPlot(gene1 = 'ENSG00000000938', 
        gene2    = 'ENSG00000001084',
        rna.expr = rnaExpr,
        metadata = metaMatrix)

GDCRNATools documentation built on Nov. 27, 2020, 2 a.m.