getFDgene: Get fitness defect genes

In PCpheno: Phenotypes and cellular organizational units

Description

Function to select genes that present a significant growth defect according to the condition(media) or generation time.

Usage

getFDgene(data,condition,cutoff,mode="generation",subset)

Arguments

data	List of fitness defect scores for genes tested at different experimental conditions.
condition	Dataframe of experimental conditions
cutoff	Numerical vector of length one or more, defining the threshold of 'significance' for the fitness defect score
mode	Character string defining the base of the selection either 'condition' (media) or 'generation' time, Default=generation.
subset	Numerical vector or list to which apply the different cutoffs.

Value

Reduced list of gene fitness scores per experimental condition according to the experimental condition or the generation time.

Author(s)

N. LeMeur

References

Giaever G. et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature. 418(6896):387-91. PMID: 12140549

Examples

 data(GiaeverPheno)
 data(GiaeverExpCdt)
 ##Select all the genes, in the different experimental conditions, that present a fitness score above 20, 100 and 100 at 5, 15 and 20 generations, respectively 
 fitnessGen <- getFDgene(GiaeverPheno,condition=GiaeverExpCdt,cutoff=c(20,100,100),mode="generation",subset=c(5,15,20))
 ##Select all the genes, that present a fitness score above 15 and 100
 ##in the condition set A and B respectively, independently of the generation time 
fitnessCondt <- getFDgene(GiaeverPheno,condition=GiaeverExpCdt,cutoff=c(100,15),mode="condition",subset=list(a=c(1:23,27,30,31),b=c(24:26,28,29)))

PCpheno documentation built on Nov. 8, 2020, 5:10 p.m.