query_snaptron_junc: Query an junction using snaptron

In dzhang32/snaptronr: Queries snaptron database for details of junctions

Description

query_snaptron_junc takes as input the junction co-ordinates and returns the details of matching junctions found in the snapton database

Usage

query_snaptron_junc(database, regions, rfilter = NULL,
  rfilter_values = NULL, method = "contains", tmp_dir = ".")

Arguments

database	Character scalar. Database of junctions - "srav1", "srav2", "gtex"
regions	Character scalar. Genomic co-ordinates of the junctions you want to query in format - "chr1:1-100"
rfilter	Character vector. Filters to use for returned junctions - "length", "strand", "annotated" etc
rfilter_values	Character vector. Corresponding to rfilter parameters, need to be prefaced by the type of test or ":" - e.g. "<:5000" or ":1"
method	Character scalar. Do you want all junctions within the region or only those precisely matching the start and stop?

Value

df with details of junctions that match criteria from snaptron

See Also

For more details on input and output parameters see: http://snaptron.cs.jhu.edu/reftables.html

Examples

query_snaptron_junc(database = "gtex", regions = "chr4:89729278-89771396",
  rfilter = c("length", "annotated"), rfilter_values = c("<:10000", ":0"))
query_snaptron_junc(database = "srav2",
  regions = c("chr4:89729278-89771396", "chr4:89729278-89729407"),
  method = "exact", tmp_dir = "/home/dzhang/")

dzhang32/snaptronr documentation built on May 16, 2019, 4:07 a.m.