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pfm
1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20
A 2  3  5  1  0 13  1  3 18  0  6  1  0  1  1  6  1  2  6  2
C 8  3  2 17 19  0 12 10  1  0  0  1  0  1 18  0 12  7  6  5
G 2 10 12  1  0  5  7  1  1 20 14 14 20 18  0 14  5  3  7  7
T 8  4  2  1  0  2  0  6  0  0  0  5  0  1  1  0  1  8  1  6

pwm <- toPWM(pfm)
pwm=PWMatrix(ID="Unknown", name=tf, matrixClass="Unknown", strand="+", bg=c(A=0.25, C=0.25, G=0.25, T=0.25), tags=list(), profileMatrix=pwm, pseudocounts=numeric())
peaks = searchSeq(pwm, seq, min.score = "80%",mc.cores=10L)
peaks_bed = as(peaks, "GRanges")

head(as.data.frame(peaks_bed$siteSeqs)$x)
[1] "AGCCCACTAGGGTGCAGTCC" "ATACCAGAAGAAGGCATCAG" "ACACCAGAAGAGGGCGTCAG"
[4] "ATGCCACGAGGTGGAGATAA" "GACTCACTAGAGGGCACAGG" "TCTACAGCAGGTGGCAACAC"

af=affinity(normalize.pwm(pwm@profileMatrix), as.data.frame(peaks_bed$siteSeqs)$x)

sum(af=='NaN')/length(af)
[1] 0.4785195

start(peaks_bed) <- start(peaks_bed) - 30
end(peaks_bed) <- end(peaks_bed) + 30
extended_seqs <- getSeq(Mmusculus, peaks_bed)
af_ext=affinity(normalize.pwm(pwm@profileMatrix),as.data.frame(extended_seqs)$x)

* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘exactgevparams’ ‘jaspar’ ‘R_affinity_multi’ ‘R_affinity_sum_multi’
Undocumented data sets:
‘exactgevparams’ ‘jaspar’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'get.affinity.cutoff'
‘cutoff’
Documented arguments not in \usage in documentation object 'get.affinity.cutoff':
‘pvalue.cutoff’
Documented arguments not in \usage in documentation object 'read.transfac':
‘dir’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... WARNING
Argument items with no description in Rd object 'evaluate.ranking':
‘ranking’ ‘seq.name2matrix’ ‘roc.plot’ ‘add’ ‘col’ ‘predictors’
Argument items with no description in Rd object 'local.paffinity':
‘affnt’ ‘pwm’ ‘seq’ ‘Rmax’ ‘lambda’ ‘pseudo.count’ ‘gc.content’
‘window.size’ ‘window.offset’