Oscope (version 1.2.0)

FlagCluster: Flag gene clusters with small within-cluster phase differences and/or small within-cluster sine scores

Description

Flag gene clusters with small within-cluster phase differences and/or small within-cluster sine scores

Usage

FlagCluster(SineRes, KMRes, Data, qt, thre=pi/4, qtincluster=.5, qtinpermu=.9 ,Seed=1)

Arguments

SineRes

output of OscopeSine() function

KMRes

output of KMRes() function

Data

a gene-by-sample (isoform-by-sample) matrix indicating the rescaled expression of genes/isoforms. all values should be between [-1, 1].

qt,thre

Define a gene pair's linear score as min(eta, pi-eta), in which eta is defined as phase shift mod pi. A cluster will be flagged if the qt th quantile of within-cluster linear score is less than thre.

qtincluster,qtinpermu

To define clusters with small within-cluster sine scores, for each cluster we generate permuted data of these genes (different cell permutation for each gene). We calculate the within-cluster sine scores within the cluster of permuted genes, then infer whether the sine scores in the cluster of interest are greater than those generated by the permuted genes. A cluster will be flagged if its qtincluster th quantile in the original data is less than its qtinpermu th quantile in permuted data.

Seed

seed

Value

Output: RemoveID: a vector of cluster numbers that are flagged; SineCompreList: sine score and permuted sine score for each cluster; LinearList: linear score of each cluster

Examples

aa <- sin(seq(0,1,.1))
bb <- sin(seq(0.5,1.5,.1))
cc <- sin(seq(0.9,1.9,.1))
tmp <- matrix(sin(rnorm(330)),ncol=11)
rownames(tmp) <- paste0("tmp",1:30)
Dat <- rbind(aa, bb, cc, tmp)
res1 <- OscopeSine(Dat)
res2 <- OscopeKM(res1, quan=.8, maxK=5)
res <- FlagCluster(res1, res2, Dat)