checkAndInitPipe: Init uORFome pipeline

In Roleren/uORFomePipe: uORF prediction in R

Init uORFome pipeline

Description

Make directory structure for orf finding, create database assign variables and validate input data.

Usage

checkAndInitPipe(
  mainPath,
  df.rfp,
  df.rna,
  df.cage,
  organism,
  biomart = "ensembl",
  mode = "uORF",
  startCodons.cds.allowed = c("ATG", "CTG", "TTG", "AAG", "AGG"),
  stopCodons.cds.allowed = c("TAA", "TGA", "TAG"),
  features = c("countRFP", "disengagementScores", "entropyRFP", "floss", "fpkmRFP",
    "ioScore", "ORFScores", "RRS", "RSS", "startCodonCoverage", "startRegionCoverage",
    "startRegionRelative")
)

Arguments

mainPath	folder for uORFome to put results
df.rfp	ORFik experiment of Ribo-seq
df.rna	ORFik experiment of RNA-seq, set to NULL if you don't have RNA-seq
df.cage	ORFik experiment of CAGE, set to NULL if you don't have CAGE.
organism	scientific name of organism, like Homo sapiens, Danio rerio, etc.
biomart	default "ensembl", get gene symbols and GO terms for uORF genes. Will be automaticly detected by organism name in ensembl database. Set to NULL if you don't want to check Gene symbols and GO terms.
mode	character, default: "uORF". alternative "aCDS". Do you want to predict on uORFs or artificial CDS. if "aCDS" will run twice once for whole length CDS and one for truncated CDS to validate model works for short ORFs. "CDS" is option to predict on whole CDS.
startCodons.cds.allowed	character, default same as startCodons argument. Which start codons can the CDS you train on have ?
stopCodons.cds.allowed	character, default same as stopCodons argument Which stop codons can the CDS you train on have ?
features	features to train model on, any of the features created during ORFik::computeFeatures, default: c("countRFP", "disengagementScores", "entropyRFP", "floss", "fpkmRFP","ioScore", "ORFScores", "RRS", "RSS", "startCodonCoverage", "startRegionCoverage","startRegionRelative")

Details

Debug possibility:
If you get this error:
Error in bmRequest(request = request, verbose = verbose) :
Internal Server Error (HTTP 500).
Rerun and it should work, this is a port issue.

Roleren/uORFomePipe documentation built on Jan. 14, 2024, 5:11 a.m.