mergeData: Function to merge different circRNA lists from CIRI 2

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

Function to merge different circRNA lists from CIRI 2

Description

This function executes the docker container ciri2merge by running the merge of different lists of circRNAs predicted by CIRI2 following a sample data files provided by the user. The function executes also a filter based on the number of back-splicing reads computed in each experiment and across replicates of the same biological condition.

Usage

mergeData(
  group = c("sudo", "docker"),
  scratch.folder,
  data.folder,
  samples.ids,
  covariates,
  covariate.order,
  extension,
  column_index
)

Arguments

group	a character string. Two options: "sudo" or "docker", depending to which group the user belongs
scratch.folder	a character string indicating the scratch folder where docker container will be mounted
data.folder	a character string indicating the data folder where the file to merge are located
samples.ids	a character vector indicating the identifiers of the samples
covariates	a character vector indicating the classes of the samples
covariate.order	a character vector indicating a vector reporting the covariate classes ordered as desidered in the output file
extension	a character string indicating the filename extension of the files that have to merge
column_index	an integer value > 1 indicating which column values have to been reported in the output file

Value

Two tab-delimited tables reporting the BS supporting reads and the coordinates of the filtered circRNAs are reported

Author(s)

Nicola Licheri and Giulio Ferrero

kendomaniac/docker4seq documentation built on April 8, 2024, 5:39 p.m.