Runs differential analyses pipeline of choice on consensus peaks
differentialAnalyses(
final.matrix,
contrasts,
experiment.type,
DA.choice,
DA.fdr.threshold,
DA.lfc.threshold,
comparison.scheme,
save.DA.peaks,
DA.peaks.path,
batch.correction,
batch.information,
additional.covariates,
sv.number,
verbose
)
Annotated Consensus peaks
user-defined contrasts for comparing samples
The type of experiment either set to "ATAC-Seq" or "RNA-Seq"
determines which pipeline to run: (1) edgeR, (2) limma-voom, (3) limma-trend, (4) DEseq2
fdr cut-off for differential analyses
log-fold change cutoff for differential analyses
either one-vs-one (OVO) or one-vs-all (OVA) comparisons.
logical, saves differentially accessible peaks to an excel file
the path which the excel file of the DA peaks will be saved, if not set it will be saved to current directory.
logical, if set will run unsupervised batch correction via sva (default) or if the batch information is known `batch.information` argument should be provided by user.
character vector, given by user.
vector or data.frame, this parameter will be directly added to design matrix before running the differential analyses, therefore won't affect the batch corrections but adjust the results in down-stream analyses.
number of surrogate variables to be calculated using SVA, best left untouched.
prints messages through running the pipeline
returns consensus peaks (batch corrected version if enabled) and DA peaks