getGeneinfo: Get Gene Informaton from a ballgown object

In VaSP: Quantification and Visualization of Variations of Splicing in Population

Description

Get gene informaton from a ballgown object by genes or by genomic regions

Usage

getGeneinfo(genes = NA, bg, chrom, start, end, samples = sampleNames(bg),
            trans.select = NA)

Arguments

genes	a character vector specifying gene IDs in 'bg'. Any values other than NA override genomic region (chrom, start, stop)
bg	ballgown object
chrom	chromosome of a region
start	start postion
end	stop postion
samples	names of samples. The transcrpts in these samples are subjected to 'trans.select'
trans.select	logical expression-like string, indicating transcript rows to select from a matrix of transcript coverages: NA value keeps all transcripts.

Value

a data.frame in bed-like file format that can be used as input for plotGenes in the SuShi package

See Also

splicePlot; plotGenes in Sushi package

Examples

data(rice.bg)
unique(geneIDs(rice.bg))

gene_id <- c('MSTRG.181', 'MSTRG.182', 'MSTRG.183')
geneinfo <- getGeneinfo(genes=gene_id,rice.bg)
trans <- table(geneinfo$name) # show how many exons each transcript has
trans

library(Sushi)
chrom = geneinfo$chrom[1]
chromstart = min(geneinfo$start) - 1e3
chromend = max(geneinfo$stop) + 1e3
color = rep(SushiColors(2)(length(trans)), trans)

par(mar=c(3,1,1,1))
plotGenes(geneinfo, chrom, chromstart, chromend, col = color, bheight = 0.2,
            bentline = FALSE, plotgenetype = 'arrow', labeloffset = 0.5)
labelgenome(chrom, chromstart , chromend, side = 1, n = 5, scale = 'Kb')

VaSP documentation built on Feb. 28, 2021, 2:02 a.m.