w_analysis {TFHAZ} | R Documentation

## 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)

[Package TFHAZ version 1.12.0 Index]