jar: Rate ratios after adding an artificial number to all features

In tgac-vumc/CSSA: Analysis and Simulation Tools for CRISPR-Cas9 Pooled Screens

Rate ratios after adding an artificial number to all features

Description

jar adds a specified number to all features of both input vectors, after which it calculates rate ratios for all features. The function was designed to prevent zeros in count data.

Usage

jar(t1, t0, n = 5, log = 2, normfun = "sum", normsubset)

Arguments

t1	Numeric vector. Feature data in test sample
t0	Numeric vector. Feature data in control sample
n	Numeric. Specify how much is added to each value before calculating rate ratios. Default = 5
log	Logical or numeric. Specify whether to log-transform the rate ratio, and with what base. If TRUE, uses natural logarithm. Default = 2
normfun	Character string. Specify with which function to standardize the data. Default = "sum"
normsubset	Integer vector. Specify the indices of features that are to be used in standardization

Value

Returns a numeric vector of the same length as the input vectors with the (log2-transformed) rate ratios after adding a specified number to all features.

Author(s)

Jos B. Poell

See Also

radjust, doublejar, ess, noness

tgac-vumc/CSSA documentation built on Oct. 10, 2022, 7:27 p.m.