Description Usage Arguments Value Examples
Given a surrogateResults object from calcNeighborMutations(), generated a 'melted' table that summarizes all surrogateMutation/sample pairs.
1 | buildSurrogateTable(surrogateResult)
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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/
1 2 3 4 5 6 7 | ##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
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