Description Usage Arguments Value Author(s) References Examples
View source: R/snaptron_query.R
This function uses the Snaptron API to query specific exon-exon junctions that are available via Intropolis as described in the vignette.
1 | 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!
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | 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)
|
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