shiftrPrepare {shiftR}

Prepare Data for Fast Circular Permutation Analysis

Description

The concept of circular permutations is symmetric with respect to the input data sets. The algorithm for circular permutation calculation is, however, not symmetric with respect to two datasets and thus the required data preprocessing is also different. For simplicity, we call the data sets 'left' and 'right'.

Usage

shiftrPrepareLeft(set)
shiftrPrepareRight(set)

Arguments

set

A 0/1 vector defining selected (genomic) features. The 'left' and 'right' sets must have equal length. The enrichment of their overlap can be assessed w ith shiftrPermBinary function.

Value

Returns objects of class fcpLeft and fcpRight respectively. The returned objects are used in singlePermutation and shiftrPermBinary functions.

Author(s)

Andrey A Shabalin [e-mail]

See Also

See codeshiftrPermBinary function and the respective example.

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)

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

### Check object sizes
# Notice asymetry in binary object sizes

object.size(lset)
object.size(rset)
object.size(lbin)
object.size(rbin)