As the title states, I'm unfortunately unable to calculate P value for several large motifs, the most important for me being CTCF motifs. I tried using several different motif databases, including both PWM and PFM from JasparCore and Hocomoco (for example: http://hocomoco11.autosome.ru/motif/CTCF_HUMAN.H11MO.0.A))
Running both TFMpv2sc() and TFMsc2pv() for these Motifs will never end and thus won't calculate respectively pvalue or required score. I don't get any error or warnings messages, just accumulation of memory usages.
#Recreate PMW matrix from CTCF hocomoco H11
CTCF <- matrix(c(-0.9579969, -0.4896964, 0.03111792, -1.269623, -3.903142,
1.02169599, -2.5837429, -0.91763116, 1.278650, -3.903142, 0.4300416,
-2.1628244, -2.818635, -1.561499, -1.269623, 0.4554168, -1.1630083, -0.9376104,
0.39339860, 0.3608849, -0.3915227, -1.06667279, 1.222080, 1.373049, -3.32473679,
0.9509855, 0.85828331, -2.484194, -3.903142, -4.4000580, -2.1628244, -3.903142,
-2.162824, 1.245093, -2.6943080, 0.8032021, 0.5185281, 0.06870117, -0.6731697,
0.7297891, 0.78894434, -1.867504, -3.903142, -0.03211744, 0.2503418, -1.18861551,
-1.488882, 1.369037, 0.8879832, 0.8481840, 1.360965, 1.226725, -2.818635, 0.8413941,
0.2625703, -0.7537887, 0.23171390, 0.5138123, -0.4517429, -0.85998235, -1.770121,
-4.400058, -1.52453126, -2.9606439, -0.06530073, -2.310655, -3.572691, -3.9031418,
0.3608849, -3.903142, -1.327521, -1.681385, -3.3247368, -1.8675043, 0.3772739,
-1.68138546), nrow=4, byrow=TRUE, dimnames=list(c("A","C", "G", "T"), c(1:19)))
#Let's say our sequence is all G's, not a very biological important example ...
score <- sum(CTCF[3,])
#calculating either pvalue for this score or score threshold
TFMPvalue::TFMsc2pv(pwm, score=score, type="PWM")
TFMPvalue::TFMpv2sc(pwm, pvalue=0.001, type="PWM")
Hi,
As the title states, I'm unfortunately unable to calculate P value for several large motifs, the most important for me being CTCF motifs. I tried using several different motif databases, including both PWM and PFM from JasparCore and Hocomoco (for example: http://hocomoco11.autosome.ru/motif/CTCF_HUMAN.H11MO.0.A))
Running both TFMpv2sc() and TFMsc2pv() for these Motifs will never end and thus won't calculate respectively pvalue or required score. I don't get any error or warnings messages, just accumulation of memory usages.
Thank you in advance for your response!
-Douwe