getGeneinfo: Get Gene Informaton from a ballgown object

In yuhuihui2011/vasp_test: Quantification and Visulization 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) - 1000
chromend = max(geneinfo$stop) + 1000
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")

yuhuihui2011/vasp_test documentation built on March 5, 2020, 12:50 a.m.