see update, please. Thank you.
• 0 views
•
link
written
by
Zhilong Jia
Position Frequency Matrix to Position Weight Matrix, whose colsums need to be 1.
In R, Biostrings::PWM can convert the Position Frequency Matrix to Position Weight Matrix (pfm to pwm). but the colsums of pwm is not 1. However, in seqLogo::makePWM request a pwm with colsum is 1. What's the reason or wrong? Is there any other way to convert the pfm to pwm since seqLogo::makePWM is of necessity for me. Thank you.
Update: Code as below.
library(Biostrings)
data(HNF4alpha)
pfm <- consensusMatrix(HNF4alpha)
#JASPAR_CORE/MA0002.2.pfm
pfm1 <- c(1387 , 2141,727,1517,56,0,0,62,346,3738,460,0,116
,1630,1060,1506,519,1199,5098,4762,1736,2729,236,0,0,1443
,851,792,884,985,3712,0,0,85,1715,920,4638,5098,3455
,1230,1105,1981,2077,131,0,336,3215,308,204,0,0,84)
pfm1 <- as.integer(pfm1)
pfm1 <- matrix(pfm1, nrow=4, ncol=13, byrow = TRUE)
rownames(pfm1) <- c("A", "C", "G", "T")
pfm[rownames(pfm1),] <- pfm1
pwm <- PWM(pfm)
colSums(pwm)
## 0.24534982 0.24245488 0.24187243 0.23899403 0.17464467 -0.15326904 -0.03531437 0.17292782 0.21962851 0.20141431 -0.03056159 -0.15326904 0.18119170
• 7,906 views
•
link
updated
by
Ram
•
written
by
Zhilong Jia
•
written
by
Zhilong Jia
2 answers
Sorry for not picking this up earlier, but if you are still following could you post an example?
I think to convert from a frequency matrix to weight matrix should be simply done by dividing all columns by their colsums. So, it might just be a rounding error, which could be introduced possibly by large colsums, but that is hard to say without example.
• 0 views
•
link
written
by
Michael Dondrup
@RamRs, @Michael, From the output. It's not the rounding error. Thank you.
• 0 views
•
link
updated
by
Ram
•
written
by
Zhilong Jia
•
written
by
Zhilong Jia
This can be calculated using prop.table function with margin=2
> a <- matrix(1:20,nr=4)
> a
[,1] [,2] [,3] [,4] [,5]
[1,] 1 5 9 13 17
[2,] 2 6 10 14 18
[3,] 3 7 11 15 19
[4,] 4 8 12 16 20
> prop.table(a,2)
[,1] [,2] [,3] [,4] [,5]
[1,] 0.1 0.1923077 0.2142857 0.2241379 0.2297297
[2,] 0.2 0.2307692 0.2380952 0.2413793 0.2432432
[3,] 0.3 0.2692308 0.2619048 0.2586207 0.2567568
[4,] 0.4 0.3076923 0.2857143 0.2758621 0.2702703
Log in to answer this question.
Hi, thanks for this. Did you find an answer to the issue above? Also, could you recommend the best way to obtain PWMs from the Jaspar collection of pfms?