Hi everyone,
so i have been doing analysis on promoters , SL_promoter_stringset is a list of 1600 promters stringsets, MotifList are a list of pfm for around 100 motifs, namely
'M0006_1.02 ' etc
i am going to see if these motifs are part of the promoters
here is my code
dllm4<-makePriors(SL_promoter_stringset,1) dllm5<-toPWM(MotifList,prior = dllm4) dllm6<-makeBackground(dllm5,bg.seq=SL_promoter_stringset,type = 'logn',bg.len = 100, bg.source = 'all at promoters split into 100bp chunks') dllm7<-motifEnrichment(sequence = SL_promoter_stringset, pwms = dllm6)
i tried to get the background and did the motifenrichment analysis, so the outcome looks something like this for
dllm7$pwms$M0006_1.02 dllm7$pwms$M0006_1.02 An object of class 'PWM' ID: M0006_1.02 Target name: M0006_1.02 Frequency matrix: $pfm [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] A 25 14 38 0 0 20 16 35 25 18 C 39 72 0 80 96 1 68 35 16 24 G 27 13 61 19 0 71 8 16 43 17 T 9 1 0 2 4 8 8 14 16 41 Position weight matrix (PWM): $pwm [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] A -0.5462997 -1.36650370 0.06497302 -6.6724253 -6.658211 -0.8630223 -1.1784698 -0.06684512 -0.5462997 -1.0121416 C 1.5401439 2.42241378 -6.64385619 2.5599365 2.836785 -3.5697404 2.3401083 1.38458592 0.2617849 0.8427707 G 1.0118105 -0.03502867 2.19806183 0.4936162 -6.658211 2.4022734 -0.7263503 0.26178490 1.6805495 0.3485468 T -1.9836158 -4.76039493 -6.64385619 -3.9824608 -3.084600 -2.1464966 -2.1464966 -1.36650370 -1.1784698 0.1592327 With background nucleotide frequencies which also serve as pseudo-count: $prior.params A C G T 0.3667722 0.1332278 0.1332278 0.3667722
i am wondering if there are any packages or any functions in bioconductor so that i can do further investigation in these motifs and mainly to visually analyse if these motifs are actually exist in these promoters (i already have a list of promoters as dnastringset) and how they interact with transcription factors. thank you very much
You may want to try motifStack or others listed or others listed under 'visualization' in biocViews.
Valerie