getFDgene {PCpheno} | R Documentation |
Function to select genes that present a significant growth defect according to the condition(media) or generation time.
getFDgene(data,condition,cutoff,mode="generation",subset)
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. |
Reduced list of gene fitness scores per experimental condition according to the experimental condition or the generation time.
N. LeMeur
Giaever G. et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature. 418(6896):387-91. PMID: 12140549
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)))