sample2experiment: generating counts, FPKM and TPM tables from rnaseqCounts...

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

generating counts, FPKM and TPM tables from rnaseqCounts outuputs

Description

This function generates counts, FPKM and TPM tables from rnaseqCounts outuputs.

Usage

sample2experiment(
  sample.folders,
  covariates,
  batch = NULL,
  bio.type = c("protein_coding", "unitary_pseudogene", "unprocessed_pseudogene",
    "processed_pseudogene", "transcribed_unprocessed_pseudogene", "processed_transcript",
    "antisense", "transcribed_unitary_pseudogene", "polymorphic_pseudogene", "lincRNA",
    "sense_intronic", "transcribed_processed_pseudogene", "sense_overlapping",
    "IG_V_pseudogene", "pseudogene", "TR_V_gene", "3prime_overlapping_ncRNA",
    "IG_V_gene", "bidirectional_promoter_lncRNA", "snRNA", "miRNA", "misc_RNA", "snoRNA",
    "rRNA", "IG_C_gene", "IG_J_gene", 
     "TR_J_gene", "TR_C_gene", "TR_V_pseudogene",
    "TR_J_pseudogene", "IG_D_gene", "ribozyme", "IG_C_pseudogene", "TR_D_gene", "TEC",
    "IG_J_pseudogene", "scRNA", "scaRNA", "vaultRNA", "sRNA", "macro_lncRNA",
    "non_coding", "IG_pseudogene"),
  output.prefix = "."
)

Arguments

sample.folders	a character string indicating the paths of rnaseqCouts output folders
covariates	a character string indicating the covariates associated to each sample. Covariates are required for differnetial expression analysis
batch	a character string indicating the batch associated to each sample
bio.type	a character string indicating the ensemb bio.type. Options: "protein_coding","unitary_pseudogene","unprocessed_pseudogene","processed_pseudogene", "transcribed_unprocessed_pseudogene","processed_transcript","antisense","transcribed_unitary_pseudogene","polymorphic_pseudogene","lincRNA","sense_intronic","transcribed_processed_pseudogene","sense_overlapping","IG_V_pseudogene","pseudogene","TR_V_gene","3prime_overlapping_ncRNA","IG_V_gene","bidirectional_promoter_lncRNA","snRNA","miRNA","misc_RNA","snoRNA","rRNA","IG_C_gene","IG_J_gene","TR_J_gene","TR_C_gene","TR_V_pseudogene","TR_J_pseudogene","IG_D_gene","ribozyme","IG_C_pseudogene","TR_D_gene","TEC","IG_J_pseudogene","scRNA","scaRNA","vaultRNA","sRNA","macro_lncRNA","non_coding","IG_pseudogene"
output.prefix	a character value indicating the output folder path

Value

Returns counts, fpkm, tpm data frames for gene and isoforms, save data frames in experiment.tables.Rda, in counts.txt, log2fpkm.txt and in log2TPM

Author(s)

Raffaele Calogero

Examples

## Not run: 
  system("wget http://130.192.119.59/public/test.samples2experiment.zip")
  unzip("test.samples2experiment.zip")
  setwd("test.samples2experiment")
  library(docker4seq)
  sample2experiment(sample.folders=c("./e1g","./e2g","./e3g",
                 "./p1g", "./p2g", "./p3g"),
                 covariates=c("Cov.1","Cov.1","Cov.1",
                 "Cov.2","Cov.2","Cov.2"),
                 bio.type="protein_coding", output.prefix=".")

## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.