sharedness {pmm} | R Documentation |
The sharedness score computes the strength of sharedness of hit genes among the conditions.
sharedness(fit, threshold = 0.2, na.action = "na.omit")
fit |
data frame returned by the |
threshold |
threshold for the false discovery rate. Genes are counted as hits if they are below this threshold. Default is 0.2. |
na.action |
a function that indicates what happens if |
The sharedness score is a combination of two quantities:
sh_g = 1/2 ( (1 - mean(fdr_cg)) + sum (fdr_cg < 1) )
The first part defines the shift away from 1 and the second part
describes how many pathogens support the shift (proportion
of FDRs < 1).
The score returns a value between 0 and 1 for each gene. Score 0 indicates that a gene is not shared among the condition and score 1 that the gene is significant among all conditions.
Anna Drewek <adrewek@stat.math.ethz.ch>
data(kinome) fit <- pmm(kinome,"InfectionIndex","weight_library") sh <- sharedness(fit, threshold = 0.2) head(sh) ## NA-Handling kinome$InfectionIndex[kinome$GeneID == 132158 & kinome$condition == "ADENO"] <- rep(NA,12) fit <- pmm(kinome,"InfectionIndex","weight_library") ## Sharedness score for genes present in all conditions sh <- sharedness(fit, threshold = 0.2, na.action = "na.omit") head(sh) ## Sharedness score for all significant genes sh <- sharedness(fit, threshold = 0.2, na.action = "use") head(sh)