Given a surrogateResults object from calcNeighborMutations(), generated a 'melted' table that summarizes all surrogateMutation/sample pairs.
buildSurrogateTable(surrogateResult)
| surrogateResult | A result object from calcNeighborMutations. |
|---|
A melted data frame with the following columns:
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"
The Gene Symbol for the surrogate gene.
The Sample name. Can be patient or cell line id.
Node Identifier of Surrogate Gene in HPRD network.
Number of neighboring mutations observed in the Sample for the surrogate gene
Total number of connections in the interaction network for the surrogate gene.
P-value from permutation analysis. Note this p-value is currently unadjusted for multiple comparisions.
Is the surrogate gene itself mutated?
##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#> ID Gene Sample NodeName #> TCGA.AO.A12D-IRS2 TCGA.AO.A12D-IRS2 IRS2 TCGA.AO.A12D IRS2(8660) #> TCGA.AO.A12D-PIK3R3 TCGA.AO.A12D-PIK3R3 PIK3R3 TCGA.AO.A12D PIK3R3(8503) #> TCGA.AO.A12D-RAF1 TCGA.AO.A12D-RAF1 RAF1 TCGA.AO.A12D RAF1(5894) #> TCGA.AO.A12D-SKP2 TCGA.AO.A12D-SKP2 SKP2 TCGA.AO.A12D SKP2(6502) #> TCGA.AO.A12D-SMARCA4 TCGA.AO.A12D-SMARCA4 SMARCA4 TCGA.AO.A12D SMARCA4(6597) #> TCGA.AO.A12D-YWHAE TCGA.AO.A12D-YWHAE YWHAE TCGA.AO.A12D YWHAE(7531) #> TCGA.BH.A0DS-CSNK2A1 TCGA.BH.A0DS-CSNK2A1 CSNK2A1 TCGA.BH.A0DS CSNK2A1(1457) #> TCGA.BH.A0DS-GSK3B TCGA.BH.A0DS-GSK3B GSK3B TCGA.BH.A0DS GSK3B(2932) #> TCGA.BH.A0DS-GTF2H1 TCGA.BH.A0DS-GTF2H1 GTF2H1 TCGA.BH.A0DS GTF2H1(2965) #> TCGA.BH.A0DS-IRS4 TCGA.BH.A0DS-IRS4 IRS4 TCGA.BH.A0DS IRS4(8471) #> TCGA.BH.A0DS-MAPK14 TCGA.BH.A0DS-MAPK14 MAPK14 TCGA.BH.A0DS MAPK14(1432) #> TCGA.E2.A1B5-GSK3B TCGA.E2.A1B5-GSK3B GSK3B TCGA.E2.A1B5 GSK3B(2932) #> TCGA.E2.A1B5-GTF2H1 TCGA.E2.A1B5-GTF2H1 GTF2H1 TCGA.E2.A1B5 GTF2H1(2965) #> TCGA.E2.A1B5-HDAC3 TCGA.E2.A1B5-HDAC3 HDAC3 TCGA.E2.A1B5 HDAC3(8841) #> TCGA.E2.A1B5-HSPCA TCGA.E2.A1B5-HSPCA HSPCA TCGA.E2.A1B5 HSPCA(3320) #> TCGA.E2.A1B5-MAPK8 TCGA.E2.A1B5-MAPK8 MAPK8 TCGA.E2.A1B5 MAPK8(5599) #> TCGA.E2.A1B5-PDGFRB TCGA.E2.A1B5-PDGFRB PDGFRB TCGA.E2.A1B5 PDGFRB(5159) #> TCGA.E2.A1B5-PTK2 TCGA.E2.A1B5-PTK2 PTK2 TCGA.E2.A1B5 PTK2(5747) #> TCGA.E2.A1B5-UBB TCGA.E2.A1B5-UBB UBB TCGA.E2.A1B5 UBB(7314) #> neighbor degree pvalue isMutated #> TCGA.AO.A12D-IRS2 4 35 0.025 1 #> TCGA.AO.A12D-PIK3R3 4 11 0.000 0 #> TCGA.AO.A12D-RAF1 7 89 0.023 0 #> TCGA.AO.A12D-SKP2 5 25 0.002 0 #> TCGA.AO.A12D-SMARCA4 5 36 0.004 0 #> TCGA.AO.A12D-YWHAE 7 58 0.001 0 #> TCGA.BH.A0DS-CSNK2A1 14 159 0.009 0 #> TCGA.BH.A0DS-GSK3B 6 59 0.028 0 #> TCGA.BH.A0DS-GTF2H1 4 26 0.014 0 #> TCGA.BH.A0DS-IRS4 4 14 0.002 0 #> TCGA.BH.A0DS-MAPK14 7 76 0.043 0 #> TCGA.E2.A1B5-GSK3B 5 59 0.035 0 #> TCGA.E2.A1B5-GTF2H1 4 26 0.007 0 #> TCGA.E2.A1B5-HDAC3 5 57 0.028 0 #> TCGA.E2.A1B5-HSPCA 6 74 0.019 0 #> TCGA.E2.A1B5-MAPK8 6 63 0.005 0 #> TCGA.E2.A1B5-PDGFRB 4 53 0.046 0 #> TCGA.E2.A1B5-PTK2 6 81 0.020 0 #> TCGA.E2.A1B5-UBB 5 55 0.022 0