SLAPE.serialPathVis: Systematic generation of heatmaps of the alteration matrices...
In saezlab/SLAPenrich: Sample-population Level Analysis of Pathway enrichments

Description Usage Arguments Note Author(s) See Also Examples

This function generates pdf files containing heatmaps of the alteration matrices for SLAPenriched pathways (with user-defined enrichment FDR and exclusive coverage) across the samples of the analysed dataset, after permuting rows and columns to highlight trend of mutual exclusivity in the alteration-patterns.

Additionally, it generates, a pdf files with three barplots indicating, for each pathway, respectively: (i) the number of mutated genes across samples; (ii) the probabilities of the pathway under consideration to be altered across samples, together with the expected number of samples with alteration in the pathway under consideration; (iii) The observed pathway alteration status across samples, together with the observed total number of samples with alteration in the pathway under consideration.

1	SLAPE.serialPathVis(EM, PFP, fdrth = 5, exCovTh = 50, PATH = "./", PATH_COLLECTION)

`EM`	A sparse binary matrix, or a sparse matrix with integer non-null entries. In this matrix the column names are sample identifiers, and the row names official HUGO gene symbols. A non-zero entry in position i,j of this matrix indicates the presence of a somatic mutations harbored by the j-sample in the i-gene. This matrix must be the same that has been inputted to the `SLAPE.analyse` function to produce the results in the `PFP` list.
`PFP`	A list containing the SLAPenrich analysis results outputted by the `SLAPE.analyse` function while analysing the genomic dataset summarised by the `EM` genomic event matrix.
`fdrth`	The false discovery rate threshold that should be used to select SLAPenriched pathways from the `PFP` list (percentage). By default in the `PFP` with an FDR < 5% are selected.
`exCovTh`	The mutual exclusivity coverage threshold that should be used to select SLAPenriched pathways from the `PFP` list (percentage). By default in the `PFP` with an exclusive coverage > 50% are selected.
`PATH`	String specifiying the path of the directory where the pdf file shoud be created.
`PATH_COLLECTION`	The pathway collection that has been tested against the `EM` dataset with the `SLAPE.analyse` function to produce the `PFP` list of results.

This function calls iteratively the SLAPE.pathvis function.

Francesco Iorio - iorio@ebi.ac.uk

SLAPE.analyse, SLAPE.pathvis

    #Loading the Genomic Event data object derived from variants annotations
    #identified in 188 Lung Adenocarcinoma patients (Ding et al, 2008)
    data(LUAD_CaseStudy_updatedGS)

    #Loading KEGG pathway gene-set collection data object
    data(SLAPE.MSigDB_KEGG_hugoUpdated)

    #Loading genome-wide total exonic block lengths
    data(SLAPE.all_genes_exonic_content_block_lengths_ensemble)

    #Running SLAPenrich analysis
    PFPw<-SLAPE.analyse(EM = LUAD_CaseStudy_ugs,
                    PATH_COLLECTION = KEGG_PATH,
                    BACKGROUNDpopulation = rownames(LUAD_CaseStudy_ugs),
                    GeneLenghts = GECOBLenghts)

    #Generating pdf files containing heatmaps of the mutual-exclusivity
    #sorted pathway alteration matrices, for an SLAPenriched pathway with
    #an exclusive coverage > 80%, and barplots with statistical scores.
    #The pdf files are saved in the current working directory.
    SLAPE.serialPathVis(EM = LUAD_CaseStudy_ugs,PFP = PFPw,
                    exCovTh = 80,fdrth = 5,
                    PATH = './',PATH_COLLECTION = KEGG_PATH)