\name{PatientSpecificGeneList} \alias{PatientSpecificGeneList} \title{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{ \item{exprslist}{Each element of \eqn{exprslist} is a list with the first element being \eqn{exprs} and the second element being \eqn{classlab}. Each row of \eqn{exprs} represents one gene and each column represents one sample. \eqn{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.} \item{alpha}{Significance level for P-value.} \item{side}{ A vector specifying the definition of P-value in each of the study, which could be either \eqn{up}, \eqn{down}, or \eqn{twosided}.} \item{type}{ A vector specifying whether the outlier pattern is \eqn{subtype} or \eqn{uniform}.} \item{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{ \item{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 \eqn{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. } \author{Yingying Wei} \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) }