singlePermutation {shiftR}

Count Feature Overlap Under a Permutation

Description

This function performs fast feature overlap count under a circular permutation. The input data sets must be preprocessed with shiftrPrepareLeft and shiftrPrepareRight functions.

Usage

singlePermutation(left, right, offset)

Arguments

left

Feature set prepared with shiftrPrepareLeft function.

right

Feature set prepared with shiftrPrepareRight function.

offset

Offset of one feature set relative to another. See the example below for clarity.
Zero indicate no offset, i.e. simply count feature overlap.

Value

Returns count of feature overlap under a circular permutation.

Author(s)

Andrey A Shabalin [e-mail]

Examples

### Number of features
nf = 1e6

### Generate left and right sets
lset = sample(c(0L,1L), size = nf, replace = TRUE)
rset = sample(c(0L,1L), size = nf, replace = TRUE) | lset

# Prepare binary sets:
lbin = shiftrPrepareLeft(lset)
rbin = shiftrPrepareRight(rset)

### count feature overlap
# R calculations
overlapS = sum(lset & rset)
# Binary calculations
overlapF = singlePermutation(lbin, rbin, 0)

message("Feature overlap: ",
        overlapS, " / ", overlapF,
        " (slow/fast count)")
stopifnot( overlapS == overlapF )


### Count overlap with offset
offset = 2017
# R calculations
overlapOS = sum(lset[ c((offset+1):nf, 1:offset)] & rset)
# Binary calculations
overlapOF = singlePermutation(lbin, rbin, offset)

message("Feature overlap at offset: ",
        overlapOS, " / ", overlapOF,
        " (slow/fast count)")
stopifnot( overlapOS == overlapOF )