A bug in calcExpectedMutations (MutationProfiling.R)

[Moriah Cohen]

There might be a problem with the input indexes for the targeting matrix resulting in a mistake in "targeting_typeOfMutation_region" calculation ...

bug:

targeting_typeOfMutation_region <- sum(targeting[regionDefinition@boundaries%in%region & mutationalPaths%in%typeOfMutation ], na.rm=TRUE )

correction:

tmp <- targeting[1:4, regionDefinition@boundaries%in%region];
tmp1 <- mutationalPaths[,regionDefinition@boundaries%in%region]
targeting_typeOfMutation_region <- sum( tmp[tmp1==typeOfMutation], na.rm=TRUE );

listExpectedMutationFrequencies[[region_mutation]] <- targeting_typeOfMutation_region

[Mohamed Uduman]

Fixed!