procExpToGene {HumanTranscriptomeCompendium} | R Documentation |
acquire a single sample from bigRNA compendium specified by accession and develop gene-level quantifications using tximport
procExpToGene(acc, tx2gene = tx2gene_gencode27(), urlprefix = "http://bigrna-test.cancerdatasci.org/data/?accession=", manifestdata = HumanTranscriptomeCompendium::load_bigrnaFiles(), regexp = "quant.sf.bz2|json")
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 |
manifestdata |
a character vector defining folders (under
|
regexp |
a character(1) regular expression for filtering
filename elements in |
the result of a tximport run
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.
# 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)