README.md

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

snapcount

Overview

snapcount is a package for interfacing with Snaptron's REST API.

Installation

# Install the development version from GitHub:
# install.packages("devtools")
devtools::install_github("langmead-lab/snapcount")

Usage

snapcount can be used with either a procedural interface

library(snapcount)

query_jx(compilation = "gtex", regions = "CD99")
#> class: RangedSummarizedExperiment 
#> dim: 3485 9662 
#> metadata(0):
#> assays(1): counts
#> rownames(3485): 28340058 28340273 ... 28352407 28352408
#> rowData names(12): DataSource:Type snaptron_id ... coverage_median
#>   source_dataset_id
#> colnames(9662): 50099 50100 ... 59759 59760
#> colData names(322): rail_id Run ... junction_coverage
#>   junction_avg_coverage
query_jx(compilation = "gtex", regions = "CD99", range_filters = samples_count == 10)
#> class: RangedSummarizedExperiment 
#> dim: 25 226 
#> metadata(0):
#> assays(1): counts
#> rownames(25): 28342638 28343346 ... 28352394 28352402
#> rowData names(12): DataSource:Type snaptron_id ... coverage_median
#>   source_dataset_id
#> colnames(226): 50117 50145 ... 59629 59713
#> colData names(322): rail_id Run ... junction_coverage
#>   junction_avg_coverage

Or using the query-builder class

sb <- SnaptronQueryBuilder$new()
sb$compilation("gtex")$regions("CD99")$query_jx()
#> class: RangedSummarizedExperiment 
#> dim: 3485 9662 
#> metadata(0):
#> assays(1): counts
#> rownames(3485): 28340058 28340273 ... 28352407 28352408
#> rowData names(12): DataSource:Type snaptron_id ... coverage_median
#>   source_dataset_id
#> colnames(9662): 50099 50100 ... 59759 59760
#> colData names(322): rail_id Run ... junction_coverage
#>   junction_avg_coverage

# sb$from_url("http://snaptron.cs.jhu.edu/gtex/bases?regions=BRCA1&sids=50099,50102,50113")$query_gene()

Reference

For more information on Snaptron please visit: http://snaptron.cs.jhu.edu/index.html.

snapcount documentation built on Nov. 8, 2020, 4:53 p.m.