Generic annotation filter

annot_filter.R

setClass("CharacterVariableFilter",
         contains = "CharacterFilter")

setClass("NumericVariableFilter",
         contains = "DoubleFilter")

VariableFilter <- function(field,
                           value,
                           condition = "==") {
    if (is.numeric(value))
        new("NumericVariableFilter",
            field = as.character(field),
            value = value,
            condition = condition)                
    else if (is.character(value))
        new("CharacterVariableFilter",
            field = as.character(field),
            value = value,
            condition = condition)
    else
        stop("Value type undefined.")
}

gene <- data.frame(foo = 1:10,
                   symbol = c(letters[1:9], "b"),
                   seq_name = paste0("chr", c(1, 4, 4, 8, 1, 2, 5, 3, "X", 4)),
                   bar = paste0(c("a", "b"), 1:10),
                   stringsAsFactors = FALSE)

doMatch <- function(x, filter) {
    do.call(condition(filter), list(x[, field(filter)], value(filter)))
}


doExtract <- function(x, filter) {
    x[doMatch(x, filter), ]
}


f1 <- VariableFilter("foo", 5, ">")

f2 <- VariableFilter("bar", "a", "startsWith")


doExtract(gene, f1)

##    foo symbol seq_name bar
## 6    6      f     chr2  b6
## 7    7      g     chr5  a7
## 8    8      h     chr3  b8
## 9    9      i     chrX  a9
## 10  10      b     chr4 b10

doExtract(gene, f2)

##   foo symbol seq_name bar
## 1   1      a     chr1  a1
## 3   3      c     chr4  a3
## 5   5      e     chr1  a5
## 7   7      g     chr5  a7
## 9   9      i     chrX  a9

Only thing is you can't use the filter expressions:

> AnnotationFilter(~ foo > 5)
Error in value[[3L]](cond) : 
  No AnnotationFilter class 'FooFilter' for field 'foo' defined