coGPS (version 1.16.0)

permCOPA: Calculate PCOPA value for permuations

Description

Run permutations by randomly shuffling the sample class labels and calculate a vector of PCOPA values for each permutation.

Usage

permCOPA(exprslist, alpha=0.05, side, type, perms=100)

Arguments

exprslist

Each element of $exprslist$ is a list with the first element being $exprs$ and the second element being $classlab$. Each row of $exprs$ represents one gene and each column represents one sample. $classlab$ is a zero-one vector indicating the status of samples. We use 0 for the baseline group, usually the normal group, and 1 for the comparison group, usually the tumor group.

alpha

Significance level for P-value.

side

A vector specifying the definition of P-value in each of the study, which could be either $up$, $down$, or $twosided$.

type

A vector specifying whether the outlier pattern is $subtype$ or $uniform$.

perms

Number of permutations to run.

Value

permResult

A matrix where each row correspond to a gene and each column correspond to one permutation.

References

Wei, Y., Hennessey, P., Gaykalova, D., Califano, J.A., Ochs, M.F., (2011) Cancer Outlier Gene Profile Sets Elucidate Pathways in Head and Neck Squamous Cell Carcinoma.

Examples

#read in data
data(Exon_exprs_matched)
data(Methy_exprs_matched)
data(CNV_exprs_matched)
data(Exon_classlab_matched)
data(Methy_classlab_matched)
data(CNV_classlab_matched)
head(Exon_exprs_matched)

#exprslist[[i]]$exprs should be in matrix format
Exon_exprs<-as.matrix(Exon_exprs_matched)
Methy_exprs<-as.matrix(Methy_exprs_matched)
CNV_exprs<-as.matrix(CNV_exprs_matched)

#exprslist[[i]]$classlab should be in vector format
Exon_classlab<-unlist(Exon_classlab_matched)
Methy_classlab<-unlist(Methy_classlab_matched)
CNV_classlab<-unlist(CNV_classlab_matched)

#make an exprslist consisting 3 studies
trylist<-list()
trylist[[1]]<-list(exprs=Exon_exprs,classlab=Exon_classlab)
trylist[[2]]<-list(exprs=Methy_exprs,classlab=Methy_classlab)
trylist[[3]]<-list(exprs=CNV_exprs,classlab=CNV_classlab)

#run 2 permutations 
perma7<-permCOPA(trylist,0.05,side=c("up","down","up"),type="subtype",perms=2)