procExpToGene {HumanTranscriptomeCompendium} | R Documentation

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

### 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)

[Package HumanTranscriptomeCompendium version 1.3.0 Index]