R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts

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Documentation for package ‘snapcount’ version 1.12.0

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snapcount-package snapcount: an R package for interfacing with Snaptron
Compilation Enum for Snaptron compilations
Coordinates Enum for Snaptron Coordinate modifiers
from_url Constructs a 'QueryBuilder' object from the given url
get_column_filters Get or set sample-related contraints for query
get_compilation Get or set query compilation
get_coordinate_modifier Get or set coordinate modifiers for the query.
get_regions Get or set query regions
get_row_filters Get or set range-related contraints for query
get_sids Get or set query sample ids
junction_inclusion_ratio Relative measure of splice variant usage similar to PSI that allows for 2 arbitrarily defined groups of junctions (not limited to cassette exons).
junction_intersection Get the intersection of junctions from 2 or more compilations which are on the same reference
junction_union Get the union of junctions from 2 or more compilations which are on the same reference
percent_spliced_in Relative measure of splice variant usage, limited currently to cassette exon splice variants
QueryBuilder Construct a QueryBuilder object given a compilation and one or regions.
query_exon Query Junctions/Genes/Exons
query_gene Query Junctions/Genes/Exons
query_jx Query Junctions/Genes/Exons
set_column_filters Get or set sample-related contraints for query
set_compilation Get or set query compilation
set_coordinate_modifier Get or set coordinate modifiers for the query.
set_regions Get or set query regions
set_row_filters Get or set range-related contraints for query
set_sids Get or set query sample ids
shared_sample_counts Shared Sample Count (SSC): counts total number of samples in which 2 different junctions both occur in.
snapcount snapcount: an R package for interfacing with Snaptron
tissue_specificity Tissue Specificity (TS): produces a list of samples with their tissues marked which either contain queried junctions (1) or not (0); can be used as input to significance testing methods such as Kruskal-Wallis to look for tissue enrichment (currently only works for the GTEx compilation).
uri_of_last_successful_request Return the URI of the last successful request to Snaptron