produce_odysse_format: Save the analysis results in odysse format

In CharlesJB/rnaseq: Wrapper Functions for RNA-Seq Post-Processing

Save the analysis results in odysse format

Description

The goal of this function is to produce de deliverables in the Odysse format. The characteristics of this format are:

* counts: A single count file for raw counts, TPM and FPKM. The anno is included in the file and each count cell contains the 3 types of counts in the <raw_counts>/<tpm>/<fpkm> format. * de: There is a file produced for each comparison. The results contains the annotations and the extra analysis (mean TPM counts and splicing analysis). There is a distinction between the fold change and the ratio where the ratio is 2^log2FoldChange and the fold change is symetrical (i.e.: ratios smaller than 1 are converted to their negative value).

Usage

produce_odysse_format(
  res,
  outdir,
  prefix,
  use_ruv = FALSE,
  digits = 4,
  force = FALSE,
  ...,
  ncores = 1
)

Arguments

res	The results obtained from the produce_deliverables function or in a similar format.
outdir	The directory where the tables will be saved
prefix	The value to add at the beginning of each lines
use_ruv	Use RUVg normalization? Needs to be pre-computed using the ruvg_normalization function. Default: FALSE.
digits	Integer indicating the number of decimal places
force	Should the files be re-created if they already exists? Default: FALSE.
...	Extra params for the format_de_results function.
ncores	Number of cores to use for de analysis. Default 1.

Details

In both cases, the results at the transcripts levels are found in the first part of the file and the results at the gene levels are found in the second part of the file.

Value

A vector of kallisto abundance filenames

Examples

abundances <- get_demo_abundance_files()

CharlesJB/rnaseq documentation built on Oct. 17, 2023, 5:37 p.m.