procExpToGene: acquire a single sample from bigRNA compendium specified by...

In vjcitn/HumanTranscriptomeCompendium: Tools to work with a Compendium of 181000 human transcriptome sequencing studies

Description

acquire a single sample from bigRNA compendium specified by accession and develop gene-level quantifications using tximport

Usage

procExpToGene(acc, tx2gene = tx2gene_gencode27(),
  urlprefix = "http://bigrna-test.cancerdatasci.org/data/?accession=",
  manifestdata = HumanTranscriptomeCompendium::load_bigrnaFiles(),
  regexp = "quant.sf.bz2|json")

Arguments

acc	character(1) sample-level accession as defined in SRA
tx2gene	a data.frame instance mapping transcript identifiers used in the compendium to gene identifiers. See note.
urlprefix	character(1) where the salmon run outputs are lodged, with acc a subfolder defined through the manifestData parameter.
manifestdata	a character vector defining folders (under results/human/27/ with salmon outputs.
regexp	a character(1) regular expression for filtering filename elements in manifestdata to define which salmon output components in the bigrna compendium are retrieved.

Value

the result of a tximport run

Note

The tx2gene_gencode function supplied with this package uses the tximportData package contents to create the data.frame for use as tx2gene. The system2 function is used to generate folders to be used by tximport.

Examples

# this example involves nontrivial internet communications
args(procExpToGene)
## Not run: 
td = tempdir()
od = getwd()
setwd(td)
nn = procExpToGene("ERX1097381")
str(nn)
setwd(od)

## End(Not run)

vjcitn/HumanTranscriptomeCompendium documentation built on Jan. 26, 2020, 11:11 a.m.