high_accumulation_zones: Finds transcription factor high accumulation DNA zones.

In DEIB-GECO/TFHAZ: Transcription Factor High Accumulation Zones

Finds transcription factor high accumulation DNA zones.

Description

This function finds transcription factor high accumulation DNA zones (TFHAZ). Starting from the accumulation vector calculated with the accumulation function, two different methods for the search of TF high accumulation DNA zones are available. The binding regions method is based on the identification of DNA regions with presence of TF binding (at least one TF) from which those with a high number of different TFs (above the threshold) are selected. This method works only if the accumulation vector is found with w=0. The overlaps method is the method used also in dense_zones function. It uses a single base local approach, identifying DNA bases, that form the dense zones, in which there is high overlap of TFs. For the binding regions method the high accumulation zones are the accumulation regions with values higher or equal to the threshold, while in the overlaps these zones are defined as sets of contiguous bases with accumulation value higher or equal to the considered threshold. The threshold value is found considering two methods. The std method considers all and only the bases of the accumulation vector (accvector) with values higher than zero, and the threshold is found with the following formula: TH = mean(accvector) + k*std(accvector). The top_perc method considers the accumulation regions and selects those in the top k percentage. In both the cases, the k is chosen by the user through the k argument. The function finds also the number of high accumulation zones, the number of total bases belonging to these zones, the minimum, maximum, mean, median and standard deviation of these zone lengths and of the distances between adjacent high accumulation zones. In the case of binding regions method, it is needed to include the data input argument, that is the GRanges object used in the accumulation function. Furhermore, in the case of single chromosome accumulation vector, the function can plots, for each chromosome base (x axis), the value of accumulation (y axis) calculated with the accumulation function. On this graph there are also shown the threshold (with a red line) and, on the x axis, the bases belonging to the high accumulation zones (with red boxes). The plot can be saved in a ".png" file.

Usage

high_accumulation_zones(accumulation, method = c("overlaps", "binding_regions"),
data, threshold = c("std","top_perc"), k, writeBed = FALSE, plotZones =
FALSE)

Arguments

accumulation	a list of four elements containing: a Rle object (or SimpleRleList) with accumulation values (e.g., obtained with the accumulation function), the accumulation type, a chromosome name, and the half-width of the window used for the accumulation count.
method	a string with the name of the method used to find high accumulation zones: "binding_regions" or "overlaps".
data	a GRanges object containing coordinates of TF binding regions and their TF name. It is needed in the case of binding regions method.
threshold	a string with the name of the method used to find the threshold value: "std" or "top_perc".
k	an integer with the percentage (with the top_perc method) or the number of std deviations (with the std method) to be used in order to find the threshold.
writeBed	When set to TRUE, for each threshold value a ".bed" file with the chromosome, genomic coordinates and accumulation values of the found dense zones is created.
plotZones	When set to TRUE, and the "accumulation" in input is calculated for a single chromosome, a ".png" file with the plot of the high accumulation zones on the accumulation vector is created.

Value

A list of nine elements:

zones	a GRanges object containing the coordinates of the high accumulation zones.
n_zones	an integer containing the number of high accumulation zones obtained.
n_bases	an integer containing the total number of bases belonging to the high accumulation zones obtained.
lengths	a vector containing the considered threshold value and min, max, mean, median and standard deviation of the high accumulation zone lengths obtained.
distances	a vector containing the considered threshold value and min, max, mean, median and standard deviation of the distances between adjacent high accumulation zones obtained.
TH	a number with the threshold value found.
acctype	a string with the accumulation type used.
chr	a string with the chromosome name associated with the accumulation vector used.
w	an integer with half-width of the window used to calculate the accumulation vector.

Examples

# loading dataset
data("Ishikawa")
# TF_acc_w_0 is in the data_man collection of datasets
# to find high accumulation zones
TFHAZ_w_0 <- high_accumulation_zones(TF_acc_w_0, method = "overlaps",
threshold = "std")

DEIB-GECO/TFHAZ documentation built on July 29, 2023, 5:45 p.m.