agg <- aggregate(Valor ~ Filial, dados, sum)
agg$Contagem <- tapply(dados$Filial, dados$Filial, FUN = length)
agg <- agg[, c(1, 3, 2)]
agg
#  Filial Contagem Valor
#1    ABC        2  1512
#2    JCT        2   610
#3    XYZ        2  1170

dados <-
structure(list(Filial = structure(c(1L, 3L, 3L, 2L, 2L, 1L), .Label = c("ABC",
"JCT", "XYZ"), class = "factor"), Matrícula = c(100L, 200L, 100L,
300L, 300L, 300L), Valor = c(500, 850, 320, 512, 98, 1012)), .Names = c("Filial",
"Matrícula", "Valor"), class = "data.frame", row.names = c(NA,
-6L))