selex.kmerPSFM {SELEX} | R Documentation |
A function used to calculate and return the PFSM (Position Specific Frequency Matrix) for a K-mer table of length k
from sample
. If an offset
value is provided, K-mer counting takes place at a fixed position within the variable region.
selex.kmerPSFM(sample, k, offset=NULL)
sample |
A sample handle to the dataset on which K-mer counting should be perfomed. |
k |
K-mer length(s) to be counted. |
offset |
Location of window for which K-mers should be counted for. If not provided, K-mers are counted across all windows. |
A K-mer table will be constructed for the specified sample
, length k
, and offset
if it does not already exist.
The output can be used by the seqLogo
package to create a sequence logo.
selex.kmerPSFM
returns a matrix containing the frequences for each base at every position.
# Build the PSFM psfm1 = selex.kmerPSFM(sample=r0, k=8, 0) # Can make sequence logos using the seqLogo package: #library(seqLogo) #seqLogo(makePWM(t(psfm1)))