Save results

SaveResults saves the results for each comparison in results. If chip = FALSE, it will also save normalized gene counts.

SaveResults(results, outpath, dds = NULL, chip = FALSE,
  method = NULL, promoters = NULL, se = NULL, txdb = NULL,
  flank.anno = FALSE, flank.dist = 5000)

Arguments

results	Either: a named list containing named lists containing DESeqResults objects for all comparisons generated by ProcessDEGs, or a DBA object from dba.analyze.
outpath	Path to directory to be used for output.
dds	A DESeqDataSet object as returned by DESeq.
chip	Boolean indicating whether results are from ChIP-seq analysis.
method	Method used for differential binding e.g. DBA_DESEQ2. Do not quote this parameter, it is a global variable from DiffBind. If a block was used, be sure to include that (e.g. DBA_DESEQ2_BLOCK).
promoters	Scalar vector containing how many basepairs up and downstream of the TSS should be used to define gene promoters.
se	Dataframe containing location informatin for super enhancers.
txdb	TxDb object to use for annotation.
flank.anno	Boolean indicating whether flanking gene information for each peak should be retrieved. Useful for broad peaks and super enhancers. Ignored if chip = FALSE.
flank.distance	Integer for distance from edges of peak to search for flanking genes. Ignored if flank.anno = FALSE.

Details

For RNA-seq results, a table will be saved for each p-value threshold, as the adj. p-value threshold affects the independent filtering step. Counts and log-fold changes will remain the same, but p-values will change slightly as different numbers of genes will be excluded from multiple testing due to low counts.