loadLIHC450k: use BiocFileCache discipline to acquire lihc450K...

In vjcitn/lihc450k: A SummarizedExperiment instance with 450k methylation data on TCGA LIHC

Description

use BiocFileCache discipline to acquire lihc450K SummarizedExperiment

Usage

  loadLIHC450k(remoteSEPath = "https://s3.amazonaws.com/biocfound-tcga/lihc450k.rds",
  remoteHSDSPath = "http://52.4.181.237:5101",
  HDF5_in_S3_Path = "https://s3.amazonaws.com/biocfound-tcga/lihc450k_imp.h5",
  hostPath = "/home/stvjc/lihc450k.h5", cache = BiocFileCache(),
  useHSDS = TRUE)

Arguments

remoteSEPath	character(1) identifying remote RDS with assay-free SummarizedExperiment instance
remoteHSDSPath	character(1) identifying HSDS server/port
HDF5_in_S3_Path	character(1) identifying file in S3 bucket with 1.2GB of HDF5 to be downloaded and cached for local use
hostPath	character(1) the data 'host' – looks strange with '/home' default but it is OK
cache	defaults to BiocFileCache() value
useHSDS	logical indicating, if TRUE, that 450k numerical data to be retrieved from HSDS; if FALSE, 1.2 GB of HDF5 will be retrieved from S3 and locally cached for future use

Note

The RDS for the SummarizedExperiment is in an AWS S3 bucket. This function will check local cache for the data and will download to cache (this is a default behavior of bfcrpath()) if not found. That download is a one-time operation for any given value of cache. Note further that the 'remoteHSDSPath' is provided courtesy of the HDF Group in early 2018 and may not be persistent.

Examples

lim = loadLIHC450k()
lim
assay(lim)
assay(lim)[1,429]
# 'confirm' with restfulSE interface to ISB-CGC
# cgcConnection() %>% tbl("DNA_Methylation_chr16") %>% 
#    filter( ParticipantBarcode=="TCGA-ZS-A9CG", Probe_Id == "cg00000029") %>% 
#    glimpse()
# Observations: ??
# Running job \:  1s:18.9 gigabytes processed
# Variables: 8                                                                  
# $ ParticipantBarcode   <chr> "TCGA-ZS-A9CG"
# $ SampleBarcode        <chr> "TCGA-ZS-A9CG-01A"
# $ SampleTypeLetterCode <chr> "TP"
# $ AliquotBarcode       <chr> "TCGA-ZS-A9CG-01A-11D-A36Y-05"
# $ Platform             <chr> "HumanMethylation450"
# $ Study                <chr> "LIHC"
# $ Probe_Id             <chr> "cg00000029"
# $ Beta_Value           <dbl> 0.65
#

vjcitn/lihc450k documentation built on May 26, 2019, 5:35 a.m.