snaptron_query {recount} | R Documentation |
This function uses the Snaptron API to query specific exon-exon junctions that are available via Intropolis as described in the vignette.
snaptron_query(junctions, version = "srav1", verbose = TRUE, async = TRUE)
junctions |
A GRanges-class object with the exon-exon junctions of interest. The chromosome names should be in UCSC format, such as 'chr1'. The strand information is ignored in the query. |
version |
Either |
verbose |
If |
async |
Defaults to |
A GRanges-class object with the results from the Snaptron query. For information on the different columns please see http://snaptron.cs.jhu.edu.
Leonardo Collado-Torres
Please cite http://snaptron.cs.jhu.edu if you use this function as Snaptron is a separate project from recount. Thank you!
library("GenomicRanges") ## Define some exon-exon junctions (hg19 coordinates) junctions <- GRanges(seqnames = "chr2", IRanges( start = c(28971710:28971712, 29555081:29555083, 29754982:29754984), end = c(29462417:29462419, 29923338:29923340, 29917714:29917716) )) ## Check against Snaptron SRA version 1 (hg19 coordinates) snaptron_query(junctions) ## Not run: ## Check another set of junctions against SRA version 2 (more data, hg38 ## coordinates) junctions_v2 <- GRanges(seqnames = "chr2", IRanges( start = 29532116:29532118, end = 29694848:29694850 )) snaptron_query(junctions_v2, version = "srav2") ## Check these junctions in GTEx and TCGA data snaptron_query(junctions_v2, version = "gtex") snaptron_query(junctions_v2, version = "tcga") ## End(Not run)