signal_at_conv: Signal between all convergent genes genome-wide

In hochwagenlab/hwglabr: Collection of R functions used in the Hochwagen Lab

Signal between all convergent genes genome-wide

Description

Deprecated! Use signal_at_intergen instead.
This function allows you to pull out the ChIP signal centered on midpoints of convergent genes. It takes as input either the wiggle data as list of 16 chromosome (output of readall_tab) or complete genome in one data frame (for example loaded from .bed files).

Usage

signal_at_conv(inputData, regionSize = 1000, saveFile = FALSE,
  inputDataFrame = FALSE)

Arguments

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.
regionSize	Number indicating the size (in bp) of the region to calculate. Defaults to 1000 bp (+/- 500 bp).
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.
inputDataFrame	Boolean indicating whether input data is a data frame. This is the case when you have data loaded from a .bed format, typically nucleosome signal, as opposed to the standard wiggle data in a list of 16 chromosomes. Defaults to FALSE.

Value

A local data frame (dplyr data frame) with three columns: chr (chromosome number), position (genome coordinate relative to midpoint of intergenic region) and signal (ChIP signal).

Examples

## Not run: 
signal_at_conv(WT)

signal_at_conv(WT, regionSize = 1500, saveFile = TRUE, inputDataFrame = FALSE)

## End(Not run)

hochwagenlab/hwglabr documentation built on Feb. 25, 2025, 5:41 a.m.