permCOPA {coGPS} | R Documentation

## 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.

### 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)

[Package coGPS version 1.24.0 Index]