plot_coverage: Coverage plot functions for DegNorm

In jipingw/DegNorm: DegNorm: degradation normalization for RNA-seq data

Coverage plot functions for DegNorm

Description

plot_coverage plots the before- and after-degradation coverage curves

Usage

plot_coverage(gene_name, coverage_output, degnorm_output, group=NULL, samples=NULL)

Arguments

gene_name	the name of the gene whose coverage coverage to be plotted.
coverage_output	CoverageClass object, the output from function coverage_cal_batch.
degnorm_output	DegNormClass object, the output from function DegNorm.
group	a vector of integers or character strings indicating the biological conditions of the samples. Coverage curves will be plotted in the same color for the same group. Default is NULL. By default all curves will plotted in different colors.
samples	a string vector for the subset of samples to be plotted. NULL means all samples to be plotted. The length of samples must be of the same length of group if both specified.

Details

plot_coverageoutputs the coverage curves before- and after-degradation normalization.

Value

The coverage curve before and after degradation normalization.

Examples

## gene named "SOD1",plot coverage curves
data(coverage_res_chr21)
data(res_DegNorm_chr21)
plot_coverage(gene_name="SOD1", coverage_output=coverage_res_chr21, 
degnorm_output=res_DegNorm_chr21, group=c(0,1,1))

jipingw/DegNorm documentation built on April 3, 2024, 1:22 a.m.