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

In shwetagopaul92/restfulSE: Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface

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

Description

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

Usage

se100k(endpoint = URL_hsds(), svrtype = "hsds",
  dsetname = "/assay001")

se1.3M(endpoint = URL_hsds(), svrtype = "hsds",
  dsetname = "/newassay001")

Arguments

endpoint	endpoint URL of remote server
svrtype	type of server, must be either 'hsds' or 'h5serv'
dsetname	complete internal path to dataset in H5 file

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

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

shwetagopaul92/restfulSE documentation built on Oct. 12, 2022, 10:51 p.m.