Description Usage Arguments Value See Also Examples
Get gene informaton from a ballgown object by genes or by genomic regions
1 2 3 4 5 6 7 8 9 | getGeneinfo(
genes = NA,
bg,
chrom,
start,
end,
samples = sampleNames(bg),
trans.select = NA
)
|
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. |
a data.frame in bed-like file format that can be used as input for
plotGenes
in the SuShi package
splicePlot
; plotGenes
in
Sushi package
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | 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")
|
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