permCOPA: Calculate PCOPA value for permuations

In coGPS: cancer outlier Gene Profile Sets

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.

Author(s)

Michael Ochs

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)

coGPS documentation built on Nov. 8, 2020, 11:11 p.m.