generateIUPACByMatrix {transite} | R Documentation

## Generates IUPAC code for motif matrix

### Description

Generates a compact logo of a motif based on IUPAC codes given by a position weight matrix

### Usage

    generateIUPACByMatrix(matrix, threshold = 0.215, code = NULL)

### Arguments

`matrix` | the position probability matrix of an RNA-binding protein
`threshold` | the threshold probability (nucleotides with lower probabilities are ignored)
`code` | if IUPAC code table has already been initialized by `initIUPAClookupTable`, it can be specified here

### Details

IUPAC RNA nucleotide code:

`A` | Adenine
`C` | Cytosine
`G` | Guanine
`U` | Uracil
`R` | A or G
`Y` | C or U
`S` | G or C
`W` | A or U
`K` | G or U
`M` | A or C
`B` | C or G or U
`D` | A or G or U
`H` | A or C or U
`V` | A or C or G
`N` | any base

### Value

the IUPAC string of the binding site

### References

http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html

### See Also

Other motif functions: `generateIUPACByKmers`, `generateKmersFromIUPAC`, `getMotifById`, `getMotifByRBP`, `getMotifs`, `getPPM`, `initIUPAClookupTable`, `motifsMetaInfo`, `setMotifs`

### Examples

    generateIUPACByMatrix(motifMatrix(getMotifById("M178_0.6")[[1]]))

[Package transite version 1.2.1 Index]