[R] Deleting rows that contain certain characters...or deleting ANOVA factors

[Crosby, Jacy R]

I'm hoping there's an easier way to do this...

I have a large matrix which looks like this (data=REG, rownames are the Pat1, Pat2,...):

	L1	L2	L3	Phen1	Phen2	Phen3
Pat1	AA	TT	A?	143	143	143
Pat2	AT	?A	AT	256	256	NA
Pat3	TA	??	TA	212	212	212
Pat4	TT	?T	AA	NA	220	220
Pat5	T?	A?	AT	98	98	98
Pat6	?A	AA	TA	113	113	113
Pat7	??	??	TT	178	178	178
Pat8	?T	?T	T?	200	NA	200
Pat9	A?	A?	A?	120	120	120
Pat10	AA	AA	T?	230	230	230

I'm performing an ANOVA: 

for(i in 1:3){
	for(j in 1:3){
		x<-summary(aov(REG[,3+j]~REG[,i], data=REG, na.act=na.exclude))[[1]][,5]  #summary()[[1]][,5] to extract p-value
		aov1[i,j]<-x[-2]   #removes the second element of pvalue...an NA
	}
}

This works fine and returns a p-value for each Phen~L model. However, I'd like to exclude cases where there is a '?' in L. I do not need these for the analysis. 

i.e. I'd like to have aov(Phen1~L1) use only Pat1-Pat4,and Pat 10.
     Similarly, aov(Phen1~L2) should use Pat1, 6, and 10.
     Etc.

Is this something I can do in the aov function, or do I need to modify my dataset before running aov? In either case, I need ideas...