singlePermutation: Count Feature Overlap Under a Permutation

In andreyshabalin/shiftR: Fast Enrichment Analysis via Circular Permutations

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 )

andreyshabalin/shiftR documentation built on May 20, 2019, 5:09 p.m.