signal_from_telomeres: Collect signal from telomeres for all chromosome arms

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

Collect signal from telomeres for all chromosome arms

Description

This function allows you to pull out the ChIP signal from all telomeres.
The function takes as input the wiggle data as a list of 16 chromosomes. (output of readall_tab).

Note: The SK1 genome annotation is currently not perfect and includes several inconsistencies at telomeric and sub-telomeric regions. This must be kept in mind when analying the data, as it will affect the output of this analysis.
Note: The fact that some sub-telomeric sequences are incomplete in the SK1 genome means that in some cases we have ChIP-seq data mapping all the way to the very end of the available sequence. This, together with the read extension performed by MACS, leads to some cases where last positions in the wiggle data for the right chromosome arms are higher than the annotated length of the respective chromosome. This results in negative position values appearing in the output of this function (typically not off by more than 150 bp). The reference SK1 sequence is not reliable in positions close to several telomeres and analyses focusing on sub-telomeric regions should only use data mapped to the S288c reference genome.

Usage

signal_from_telomeres(inputData, lengthToCollect = 1e+05)

Arguments

inputData	As a list of the 16 chr wiggle data (output of readall_tab). No default.
lengthToCollect	Number specifying the length (in bp) of the region to collect signal for, starting form the telomeres. Defaults to 100000 (i.e. 100 kb).

Value

A list with two elements, each one is itself a list containing the collected signal separately for the right and left arms of the included chromosomes:

1. small_chrs List of data frames of collected signal for right and left arms of chromosomes 1, 3 and 6

2. large_chrs List of data frames of collected signal for right and left arms of remaining chromosomes

Each data frame has two columns:

1. distance_to_telomere Distance to telomere in bp

2. signal ChIP-seq signal

Examples

## Not run: 
signal_from_telomeres(WT)

signal_from_telomeres(WT, lengthToCollect = 50000)

## End(Not run)

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