se100k: Convenience functions using EC2 server to extract tenx...

Description Usage Arguments Value Note Examples

View source: R/demos.R

Description

Convenience functions using EC2 server to extract tenx neurons full or subset data

Usage

1
2
3
4
se100k(url = "http://h5s.channingremotedata.org:5000",
  tag = "tenx_100k_sorted")

se1.3M(url = "http://h5s.channingremotedata.org:5000", tag = "tenx_full")

Arguments

url

server URL

tag

string giving the internal dataset name

Value

RESTfulSummarizedExperiment

SummarizedExperiment instance

Note

se1.3M provides access to the full 1.3 million neurons with features in their order as given in the original HDF5 while se100k provides access to only 100k neurons with expression features sorted by genomic location

Examples

1
2
3
4
5
6
7
8
ss = se100k()
# get a set of genes from Tasic et al. 2016 Nature Neuroscience
tc = tasicCortex()
adultCort = tc$GENEID
# subset
csums = apply(assay(ss[adultCort,1:500]),1,sum)
names(csums) = tc$SYMBOL
csums

restfulSE documentation built on May 2, 2018, 3:31 a.m.