merge_experiment.RNAseq: Rough merger of RNAseq experiments

In madhulika-EBI/Batchevaluation: Toolkit for batch correction

Rough merger of RNAseq experiments

Description

The function merge_experiments merges all the experiments in the list in a single experiment object and doesn't perform any correction. This function has two additional arguments log and filter (set to TRUE by default).

Usage

merge_experiment.SummarizedExperiment(
  experiments,
  filter.unexpressed.genes = TRUE,
  log,
  force = FALSE
)

Arguments

experiments	A list of wrapped experiments.
filter.unexpressed.genes	A logical indicating if the genes that are unexpressed across all the samples of a batch shall be removed. This is for the proper functioning of the current version of ComBat in correct_batch_effect.
log	A logical ndicating of whether the data shall be log-transformed(recommended).
force	A logical. If the experiments of the list are of different classes, the function is stopped, unless force=TRUE.

Value

Single SummarizedExperiment

Note

Caution: Sometime during merging experiments, phenodata (SDRF) file gets corrupted, it is advised to always check meta-data before proceeding further.

madhulika-EBI/Batchevaluation documentation built on Jan. 27, 2023, 5:27 p.m.