Code:
write.table(MU.Cost,paste("C:/RAU/R",as.character(MU.Cost$Run.Id[1]),"."
,as.character(MU.Cost$MU.Id[1]),".MU.PRICE.OUTPUT.txt",sep=""),append =
FALSE,quote = FALSE,sep = ",",row.names=FALSE)

Output:
Run.Id,MU.Id,Class,Av,lower,upper,Count.WO,Count.Seq,Total.WO.Value,Note
s
32,158,   1,   0.00,   0.00,   0.00,  0,  0,     0.0,notes
32,158,   2,  78.27,   0.00,   0.00,  8,  8,     1.1,notes
32,158,   3,  58.52,  53.96,   3.09,  5, 75,    89.1,notes
32,158,   4,   0.00,   0.00,   0.00,  0,  0,     0.0,notes
32,158,  12,  23.27,   0.00,   0.00,  8,  8,     1.1,notes
32,158,  34,  58.52,  18.96,  63.09, 75, 75,    89.1,notes
32,158, 123,  26.10,  33.13,  39.08,213,213,    90.3,notes
32,158,1234,2001.10,2000.13,2111.08,213,213,111110.3,notes

Morten Wennerberg
Business Analyst 
Commercial Frameworks

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