buildSurrogateTable: Build melted surrogate table from surrogateResults.
In laderast/surrogateMutation: Surrogate Mutations in Cancer Cells and Patients

Description Usage Arguments Value Examples

Given a surrogateResults object from calcNeighborMutations(), generated a 'melted' table that summarizes all surrogateMutation/sample pairs.

1	buildSurrogateTable(surrogateResult)

surrogateResult

A result object from calcNeighborMutations.

A melted data frame with the following columns:

`ID`	The ID for the row, which is the SampleName and Surrogate gene pasted together. For example, for the sample TCGA.A1.A0SD and the gene ABL1 pair, the id would "TCGA.A1.A0SD-ABL1"
`Gene`	The Gene Symbol for the surrogate gene.
`Sample`	The Sample name. Can be patient or cell line id.
`NodeName`	Node Identifier of Surrogate Gene in HPRD network.
`neighbor`	Number of neighboring mutations observed in the Sample for the surrogate gene
`degree`	Total number of connections in the interaction network for the surrogate gene.
`pvalue`	P-value from permutation analysis. Note this p-value is currently unadjusted for multiple comparisions.
`isMutated`	Is the surrogate gene itself mutated?

This surrogate table is used as one of the inputs to the Shiny interactive heatmap. For an example of the interactive heatmap, please visit: https://tladeras.shinyapps.io/surrogateShiny/

##load surrogate result object
data(surrogateResult)
surrogateTable <- buildSurrogateTable(surrogateResult)

##filter the surrogate table based on p-value and return surrogate mutations greater than 5.
filteredSurrTable <- surrogateTable[surrogateTable$pvalue < 0.05 & surrogateTable$neighbor > 3,]
filteredSurrTable