selex.revcomp {SELEX} | R Documentation

## Create forward-reverse complement data pairs

### Description

A function used to find and return the reverse complement of K-mers and the values associated with them. It is useful for calculating forward/reverse complement symmetrized values.

### Usage

    selex.revcomp(kmer,value)

### Arguments

`kmer` | A string array representing K-mers.
`value` | An array of associated values.

### Details

`selex.revcomp` finds and returns the reverse complement and associated value of every input K-mer, if it exists. If a reverse complement does not exist for a given K-mer, it is removed from the output. For example, consider the following K-mer and value arrays:

ACGT |  | .34
GCTA |  | .22
CGAC |  | .98
TAGC |  | .19

The output of `selex.revcomp` will be:

ACGT |  | .34 |  | ACGT |  | .34
GCTA |  | .22 |  | TAGC |  | .19
TAGC |  | .19 |  | GCTA |  | .22

### Value

`selex.revcomp` returns a data frame containing the original K-mers and values, along with their reverse complements and associated values.

### See Also

`selex.affinities`, `selex.counts`

### Examples

    # Find round 2 affinities
    r2Aff = selex.affinities(sample=r2, k=10, markovModel=mm)

    # Find the reverse complement affinities and standard errors
    Aff = selex.revcomp(kmer=r2Aff$Kmer, value=r2Aff$Affinity)
    SE = selex.revcomp(kmer=r2Aff$Kmer, value=r2Aff$SE)

    # Find the forward/reverse complement symmetrized Affinity and SE values
    symAff = (Aff$Value+Aff$Reverse.Complement.Values)/2
    symSE = sqrt((SE$Value^2+SE$Reverse.Complement.Values^2)/2)

    # Final Result
    final = data.frame(Kmer=Aff$Kmer, Affinity=Aff$Value,
      SymmetrizedAffinity=symAff/max(symAff), SE=SE$Value,
      SymmetrizedSE=symSE/max(symAff))
    final = final[order(-final$SymmetrizedAffinity),]

[Package SELEX version 1.18.0 Index]