Query Snaptron to get data from exon-exon junctions present in Intropolis

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.

snaptron_query(junctions, version = "srav1", verbose = TRUE, async = TRUE)

Arguments

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 srav1, srav2, gtex or tcga. SRA Version 1 of Intropolis has the exon-exon junctions from about 20 thousand RNA-seq samples in hg19 coordinates. SRA Version 2 has the data from about 50 thousand RNA-seq samples aligned to hg38. GTEx has about 30 million junctions from about 10 thousand samples from the GTEx consortium on hg38 coordinates. Finally, TCGA has about 36 million junctions from about 11 thousand samples from the TCGA consortium on hg38 coordinates.

verbose

If TRUE status updates will be printed.

async

Defaults to TRUE but in some situations it might be preferrable to set it to FALSE. This argument gets passed to getURL. Check https://github.com/ChristopherWilks/snaptron/issues/11 for more details.

Value

A GRanges-class object with the results from the Snaptron query. For information on the different columns please see http://snaptron.cs.jhu.edu.

References

Please cite http://snaptron.cs.jhu.edu if you use this function as Snaptron is a separate project from recount. Thank you!

Author

Leonardo Collado-Torres

Examples


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)
#> 2024-05-21 17:45:52.432963 querying Snaptron
#> 2024-05-21 17:45:52.461954 processing results
#> 2024-05-21 17:45:52.462477 found no exon-exon junctions in Intropolis version srav1 matching your query: this version uses hg19 coordinates.
#> NULL
if (FALSE) {
## 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")
}