w_analysis: Shows the number of dense zones obtained with different...

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

Shows the number of dense zones obtained with different values of base neighborhood window width.

Description

This function is used to plot the number of dense zones and the total number of bases belonging to these dense zones present in a set of inputs, obtained (all with accumulation threshold=1) using the dense_zones function, for the same accumulation type, same chromosome, and different values of w half-width of the window defining the neighborhood of each base. The plot (with x axis logarithmic-scale) is generated only if all input data refer to the same accumulation type, otherwise an error message appears. Beside helping in comparing results obtained with different values of w, this function supports finding the best value of w to be used in further analysis.

Usage

w_analysis(input_list, chr = NULL)

Arguments

input_list	a list containing multiple outputs of the dense_zones function, obtained for the same accumulation type, same chromosome and different values of w.
chr	optional argument, needed if the input was found with chr = "all"; a string or a vector containing strings with the name of the chromosome(s) (e.g., "chr1" or c("chr1", "chr4")) to be considered

Value

None, the function is invoked for its side effect.

Examples

# loading data
data("data_man")
# l is a list with dense zone (e.g., TF_dense_w_10, TF_dense_w_100,
# TF_dense_w_1000 and TF_dense_w_10000) objects present in data_man
# collection of datasets
l <- list(TF_dense_w_10, TF_dense_w_100, TF_dense_w_1000,
TF_dense_w_10000)
# plot
w_analysis(l)

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