Runs differential analyses pipeline of choice on consensus peaks
Usage
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
)Arguments
- final.matrix
Annotated Consensus peaks
- contrasts
user-defined contrasts for comparing samples
- experiment.type
The type of experiment either set to "ATAC-Seq" or "RNA-Seq"
- DA.choice
determines which pipeline to run: (1) edgeR, (2) limma-voom, (3) limma-trend, (4) DEseq2
- DA.fdr.threshold
fdr cut-off for differential analyses
- DA.lfc.threshold
log-fold change cutoff for differential analyses
- comparison.scheme
either one-vs-one (OVO) or one-vs-all (OVA) comparisons.
- save.DA.peaks
logical, saves differentially accessible peaks to an excel file
- DA.peaks.path
the path which the excel file of the DA peaks will be saved, if not set it will be saved to current directory.
- batch.correction
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.
- batch.information
character vector, given by user.
- additional.covariates
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.
- sv.number
number of surrogate variables to be calculated using SVA, best left untouched.
- verbose
prints messages through running the pipeline