differentialAnalyses {cinaR}

Differential Analyses

Description

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

Value

returns consensus peaks (batch corrected version if enabled) and DA peaks