ProcessDBRs: Extract, visualize, and save DBRs
In j-andrews7/AndrewsBCellLymphoma: One-liner RNA-seq and ChIP-seq Analyses

Description Usage Arguments Details Author(s) See Also

ProcessDBRs wraps several plotting functions to generate figures specifically for differentially bound regions in a given comparison.

ProcessDBRs(
  results,
  outpath,
  txdb,
  fdr.thresh = 0.05,
  fc.thresh = 1,
  method = NULL,
  promoters = c(-2000, 2000),
  breaks = c(seq(-3, -1.0001, length = 250), seq(-1, -0.1, length = 250), seq(-0.0999,
    0.0999, length = 1), seq(0.1, 1, length = 250), seq(1.0001, 3, length = 250)),
  heatmap.colors = NULL,
  heatmap.preset = NULL,
  reverse = FALSE,
  plot.enrich = TRUE,
  enrich.libs = c("GO_Molecular_Function_2018", "GO_Cellular_Component_2018",
    "GO_Biological_Process_2018", "KEGG_2019_Human", "Reactome_2016", "BioCarta_2016",
    "Panther_2016"),
  flank.anno = TRUE,
  flank.dist = 5000
)

`results`	`DBA` object as returned by `dba.analyze`.
`outpath`	Path to directory to be used for output.
`txdb`	`TxDb` object to use for annotation.
`fdr.thresh`	Number or numeric scalar indicating the false discovery rate (FDR) cutoff(s) to be used for determining "significant" differential binding. If multiple are given, multiple tables/plots will be generated using all combinations of `fdr.thresh` and `fc.thresh`.
`fc.thresh`	Number or numeric scalar indicating the log2 fold-change cutoff(s) to be used for determining "significant" differential binding. If multiple are given, multiple tables/plots will be generated using all combinations of `padj.thresh` and `fc.thresh`.
`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 Do not quote this parameter, it is a global variable from `DiffBind`.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.
`breaks`	Vector of sequences to be used as breaks for signal heatmaps.
`heatmap.colors`	Character vector containing custom colors to use for heatmaps in hex (e.g. `c("#053061", "#f5f5f5", "#67001f")`).
`heatmap.preset`	String indicating which of the color presets to use in heatmaps. Available presets (low to high) are: "BuRd" Blue to red. "OrPu" Orange to purple. "BrTe" Brown to teal. "PuGr" Purple to green. "BuOr" Sea blue to orange.
`reverse`	Boolean indicating whether to flip heatmap color scheme (high color will become low, etc).
`plot.enrich`	Boolean indicating whether enrichment analyses for DBRs should be run and plotted for each comparison.
`enrich.libs`	A vector of valid `enrichR` libraries to test the genes against.
`flank.anno`	Boolean indicating whether flanking gene information for each peak should be retrieved. Useful for broad peaks and super enhancers.
`flank.distance`	Integer for distance from edges of peak to search for flanking genes. Ignored if `flank.anno = FALSE`. Available libraries can be viewed with `listEnrichrDbs` from the `enrichR` package.

ProcessDBRs is called by RunDiffBind but can also be re-run with the RunDiffBind output if you want to save time and don't need to generate all of the EDA/consensus figures again.

This function will generate many figures in addition to saving the results as tables.

Jared Andrews

RunDiffBind, for generating input for this function.

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