Description Usage Arguments Details Value Examples
View source: R/genomicElementUpSetR.R
Prepare data for upset plot for genomic element distribution
1 2 3 4 5 6 7 8 9 10 11 12 | genomicElementUpSetR(
peaks,
TxDb,
seqlev,
ignore.strand = TRUE,
breaks = list(distal_upstream = c(-1e+05, -10000, -1, 1), proximal_upstream =
c(-10000, -5000, -1, 1), distal_promoter = c(-5000, -2000, -1, 1), proximal_promoter
= c(-2000, 200, -1, 0), `5'UTR` = fiveUTRsByTranscript, `3'UTR` =
threeUTRsByTranscript, CDS = cds, exon = exons, intron = intronsByTranscript,
gene_body = genes, immediate_downstream = c(0, 2000, 1, 1), proximal_downstream =
c(2000, 5000, 1, 1), distal_downstream = c(5000, 1e+05, 1, 1))
)
|
peaks |
peak list, GRanges object or a GRangesList. |
TxDb |
an object of |
seqlev |
sequence level should be involved. Default is all the sequence levels in intersect of peaks and TxDb. |
ignore.strand |
logical. Whether the strand of the input ranges should be ignored or not. Default=TRUE |
breaks |
list. A list for labels and sets for the genomic elements. The element could be an S4 method for signature 'TxDb' or a numeric vector with length of 4. The three numbers are c(upstream point, downstream point, promoter (-1) or downstream (1), remove gene body or not (1: remove, 0: keep)). |
The data will be calculated by for each breaks. No precedence will be considered.
list of data for plot.
1 2 3 4 5 6 7 8 9 10 11 12 13 | if (interactive() || Sys.getenv("USER")=="jianhongou"){
data(myPeakList)
if(require(TxDb.Hsapiens.UCSC.hg19.knownGene)){
seqinfo(myPeakList) <-
seqinfo(TxDb.Hsapiens.UCSC.hg19.knownGene)[seqlevels(myPeakList)]
myPeakList <- GenomicRanges::trim(myPeakList)
myPeakList <- myPeakList[width(myPeakList)>0]
x <- genomicElementUpSetR(myPeakList,
TxDb.Hsapiens.UCSC.hg19.knownGene)
library(UpSetR)
upset(x$plotData, nsets=13, nintersects=NA)
}
}
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.