coGPS (version 1.16.0)

PatientSpecificGeneList: Patient Specific outlier gene list

Description

Generate an outlier gene list for each patient restricted to the top PCOPA scored genes

Usage

PatientSpecificGeneList(exprslist, alpha, side, type,TopGeneNum)

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 $uniform$.

TopGeneNum

a number specifying the top number of outlier genes scored by PCOPA to be included in the generation of individual outlier gene list for each patient.

Value

outliergene_bypatient

a list whose length equals the number of tumor samples (patients). each element of the list is a list of length equaling to the length of $exprslist$, in other words the number of studies(or data type), showing the outlier gene for each patient in each study (or data type)

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)

#generate an outlier gene list for each patient restricted to the top PCOPA scored genes
IndividualList7<-PatientSpecificGeneList(trylist,0.05,side=c("up","down","up"),type="subtype",TopGeneNum=100)