HoneyBADGER_plotGexpProfile: Plot gene expression profile

In JEFworks/HoneyBADGER: HMM-integrated Bayesian approach for detecting CNV and LOH events using single-cell RNA-seq data

Description

Plot gene expression profile

Arguments

gexp.norm.sub	Optional normalized gene expression matrix. If not provided, internal normalized gene expression matrix is used.
chrs	Chromosomes to be plotted (default: paste0('chr', c(1:22, 'X')))
window.size	Window size for sliding window mean. Must be odd number. (default: 101)
zlim	Limit for plotting heatmap (default: c(-2,2))
setOrder	Boolean for whether or not to order cells (default: FALSE)
setWidths	Boolean for whether or not to adjust widths of chomosomes based on number of genes. Otherwise uniform size. (default: FALSE)
order	Order of cells (default: NULL)
defailt	Boolean for whether to return detailed smoothed profiles (default: FALSE)

Examples

data(gexp)
data(ref)
require(biomaRt) ## for gene coordinates
mart.obj <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", 
    dataset = 'hsapiens_gene_ensembl', 
    host = "jul2015.archive.ensembl.org")
hb <- HoneyBADGER$new()
hb$setGexpMats(gexp, ref, mart.obj, filter=FALSE, scale=FALSE)
hb$plotGexpProfile() 

JEFworks/HoneyBADGER documentation built on July 24, 2021, 3:01 p.m.