call_sig_reg {sharpr2}

call_sig_reg

Description

Given an object returned from the sharpr2 function, this function calls significant regions that contain driver elements for a specific tiled region based on a user-defined threshold.

Usage

call_sig_reg(res, nr, threshold = 3.5, win = 10)

Arguments

res

An object obtained from the sharpr2 function.

nr

An integer indicating the number of tiled region in res for which driver elements will be called.

threshold

The cutoff to identify driver elements in the tiled region. The positions with a z-score larger than the threshold will be called. The default is 3.5.

win

A window size for removing sporadic significant regions. If a significant consecutive region is small than win, it will be treated as false signals. The default is 10.

Value

sig_reg: identified regions containing driver elements.

motif: predicted 20bp core driver elements

Examples

data(hidra_ex)
re  <- sharpr2(hidra_ex[1:2000,], l_min = 150, l_max = 600, f_dna = 5, f_rna = 0, sig=TRUE)
call_sig_reg(re,850, threshold=2.5)