SaveResults: Save results
In j-andrews7/AndrewsBCellLymphoma: One-liner RNA-seq and ChIP-seq Analyses

Description Usage Arguments Details Author(s)

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
)

`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 Do not quote this parameter, it is a global variable from `DiffBind`.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`.

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.

Jared Andrews

j-andrews7/AndrewsBCellLymphoma documentation built on Sept. 9, 2021, 11 a.m.