GitHub - langmead-lab/snapcount: R Package for interfacing with Snaptron for rapid querying of expression counts (original) (raw)

snapcount

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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.