signal_at_intergen: Signal at intergenic regions between convergent, divergent or...
In luisvalesilva/hwglabr: Collection of R functions used in the Hochwagen Lab

Description Usage Arguments Value Examples

This function allows you to pull out the ChIP signal over a window of positions of the selected size (defaulting to regionSize = 1000) centered on midpoints of intergenic regions between genes of the selected orientation: convergent, divergent or tandem. It takes as input either the wiggle data as list of 16 chromosome (output of readall_tab) or the complete genome in one data frame (for example loaded from .bed files).

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signal_at_intergen(inputData, inputDataFrame = FALSE,
  orientation = c("conv", "div", "tandem"), regionSize = 1000,
  includeOverlapping = TRUE, saveFile = FALSE)

`inputData`	As a list of the 16 chr wiggle data (output of `readall_tab`) or a data frame (in which case you must set `inputDataFrame = TRUE`). No default.
`inputDataFrame`	Boolean indicating whether input data is a data frame, as opposed to the standard wiggle data in a list of 16 chromosomes. Defaults to `FALSE`.
`orientation`	A string indicating the type of intergenic region to analyze, according to the orientation of the flanking genes. Accepts one of: `conv` Convergent genes `div` Divergent genes `tandem` Tandem genes. All regions in output will be in the same 5' -> 3' orientation (genes on Crick strand are reversed). Abbreviated arguments (down to as short as the first letter only) are accepted. Defaults to `conv`.
`regionSize`	Number indicating the size (in bp) of the region to calculate. Defaults to 1000 bp (midpoint +/- 500 bp).
`includeOverlapping`	Boolean indicating whether intergenic regions between overlapping genes should be included in the analysis. If `includeOverlapping = FALSE`, intergenic regions between overlapping genes will not be included in the analysis. Otherwise all regions are included. Defaults to `TRUE`.
`saveFile`	Boolean indicating whether output should be written to a .txt file (in current working directory). If `saveFile = FALSE`, output is returned to screen or an R object (if assigned). Defaults to `FALSE`.

A local data frame (dplyr data frame) with four columns:

chr Chromosome number
position Nucleotide coordinate (relative to midpoint of intergenic region)
signal ChIP signal
dist_apart Distance between the two genes (negative value for overlapping genes)

## Not run: 
signal_at_intergen(WT)

signal_at_intergen(WT, orientation = 'div', inputDataFrame = TRUE, regionSize = 1500,
                   includeOverlapping = FALSE, saveFile = TRUE)

## End(Not run)