pseudocount_adjust: PFM/PWM Pseudo-count adjustment to get rid of 0 entries.

In kkdey/Logolas: EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices

Description

Building a pseudo-count adjusted matrix from a PWM (positional weight matrix) or a PFM (positional frequency matrix) with 0 entries.

Usage

pseudocount_adjust(table, pseudocount = NULL)

Arguments

table	A table (PFM/PWM) with the symbols along the rows and the logo stack positions along the columns, possibly containing 0 values.
pseudocount	A small pseudocount to be added mainly to bypass 0 entries. Default is NULL. If table is a counts matrix, the default changes to 0.5, if table is a positional weight matrix, the default becomes 0.001 times the minimum non-zero value of the table.

Value

Returns a new table that pseudo-count adjusts the 0 values.

Examples

data("mutation_sig")
pseudocount_adjust(mutation_sig)

kkdey/Logolas documentation built on May 20, 2019, 10:30 a.m.