R/getOffsets.r

In shiftR: Fast Enrichment Analysis via Circular Permutations

minOffset = function(n, margin){
    as.integer(ceiling(n*margin));
}

maxOffset = function(n, margin){
    as.integer(floor(n*(1-margin)));
}

getNOffsetsMax = function(n, margin){
    maxOffset(n, margin) - minOffset(n, margin) + 1L;
}

getOffsetsAll = function(n, margin){
    stopifnot( is.numeric(margin) );
    stopifnot( margin >= 0 );
    stopifnot( margin < 0.5 );
    stopifnot( is.numeric(n) );
    return( ceiling(n*margin):as.integer(n*(1-margin)) );
}

getOffsetsRandom = function(n, npermute, margin = 0.05){
    stopifnot( is.numeric(margin) );
    stopifnot( margin >= 0 );
    stopifnot( margin < 0.5 );
    stopifnot( is.numeric(n) );
    stopifnot( is.numeric(npermute) );
    npermute = floor(npermute);
    maxo = getNOffsetsMax(n, margin);
    if( npermute < maxo){
        offsets = sample.int(n = maxo, size = npermute, replace = FALSE) +
                    (minOffset(n, margin) - 1L);
    } else {
        offsets = getOffsetsAll(n, margin);
    }
    return( offsets );
}

getOffsetsUniform = function(n, npermute, margin = 0.05){
    stopifnot( is.numeric(margin) );
    stopifnot( margin >= 0 );
    stopifnot( margin < 0.5 );
    stopifnot( is.numeric(n) );
    stopifnot( is.numeric(npermute) );
    fr = minOffset(n, margin);
    to = maxOffset(n, margin);
    stopifnot( npermute <= to - fr + 1);
    offsets = as.integer(seq.int(from = fr, to = to, length.out = npermute));
    return( offsets );
}