generalizedFC: generalized fold change

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

generalized fold change

Description

calculate the mean difference in a set of predefined quantiles of the logarithmic

Usage

generalizedFC(x, ...)

## Default S3 method:
generalizedFC(x, y, base = 10, steps = 0.05, pseudo = 1e-05, ...)

## S3 method for class 'formula'
generalizedFC(x, data, subset, na.action, ...)

Arguments

x	numeric vector, numeric vector of data values or formula, example 'Ozone ~ Month', Ozone is a numeric variable giving the data values ‘Month’ a factor giving the corresponding groups.
...	additional arguments.
y	numeric vector, numeric vector of data values
base	a positive or complex number, the base with respect to which logarithms are computed, default is 10.
steps	positive numeric, increment of the sequence, default is 0.05.
pseudo	positive numeric, avoid the zero for logarithmic, default is 0.00001.
data	data.frame, an optional matrix or data frame,containing the variables in the formula.
subset	(similar: see 'wilcox.test')an optional vector specifying a subset of observations to be used.
na.action	a function which indicates what should happen when the data, contain 'NA's. Defaults to 'getOption("na.action")'.

Value

list contained gfc, the mean and median of different group.

Author(s)

Shuangbin Xu

Examples

set.seed(1024)
data <- data.frame(A=rnorm(1:10,mean=5), 
                   B=rnorm(2:11, mean=6), 
                   group=c(rep("case",5),rep("control",5))) 
generalizedFC(B ~ group,data=data)
generalizedFC(x=c(1,2,3,4,5),y=c(3,4,5,6,7))

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.