SLAPE.write.table: Writing SLAPenrich results in a csv file
In saezlab/SLAPenrich: Sample-population Level Analysis of Pathway enrichments

Description Usage Arguments Author(s) See Also Examples

This function takes in input a list of results outputted by the SLAPE.analyse, selects enriched pathways according to user-defined significance and mutual exclusivity coverage thresholds and creates an easy to explore csv file with selected enriched pathways.

SLAPE.write.table(PFP,
                  EM,
                  filename = "",
                  fdrth = Inf,
                  exclcovth = 0,
                  PATH_COLLECTION,
                  GeneLenghts)

`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.
`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.
`filename`	String specifiying the path of the csv file to be created (including its name).
`fdrth`	The false discovery rate threshold that should be used to select SLAPenriched pathways from the `PFP` list (percentage). By default all the pathway included in the `PFP` list are selected.
`exclcovth`	The mutual exclusivity coverage threshold that should be used to select SLAPenriched pathways from the `PFP` list (percentage). By default all the pathway included in the `PFP` list are selected.
`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.
`GeneLenghts`	The named vector containing the genome-wide total exonic block lengths that has been used by the `SLAPE.analyse` function to produce the `PFP` list of results.

Francesco Iorio - iorio@ebi.ac.uk

SLAPE.analyse

    #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)
                  
    #Selecting pathway enriched at a 5% FDR,
    #that have a 50% mutual exclusivity coverage and writing them
    #in a csv file
    SLAPE.write.table(PFP = PFPw,
                      EM = LUAD_CaseStudy_ugs,
                      filename = "./LungDS_KEGG_enrichments.csv",
                      fdrth=5, exclcovth = 50, PATH_COLLECTION = KEGG_PATH,
                      GeneLenghts = GECOBLenghts)