Question

Conversion of pfm to pwm using PWM()

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Ravi Karra ▴ 140

@ravi-karra-4463

Last seen 10.2 years ago

Hi, I am trying to find TF binding sites in a set of promoters using position frequency matrices (pfm's) from jaspar and transfac. I have gotten this to work before on my machine at home, but cannot seem to get this to run on campus. I am not sure why I get the following error as I thought PWM can handle integer pfm's. Any thoughts? Thanks in advance, Ravi Code: > library (Biostrings) > pfm [,1] [,2] [,3] [,4] [,5] [,6] A 13 0 50 1 13 6 C 14 0 2 0 6 16 G 15 53 0 1 25 22 T 11 0 1 51 9 9 > typeof (pfm) [1] "integer" > pwm = pfm (PWM) Error: could not find function "pfm" > library (Biostrings) > pfm [,1] [,2] [,3] [,4] [,5] [,6] A 13 0 50 1 13 6 C 14 0 2 0 6 16 G 15 53 0 1 25 22 T 11 0 1 51 9 9 > typeof (pfm) [1] "integer" > PWM (pfm) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "PWM", for signature "matrix" > sessionInfo () R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] doMC_1.2.1 multicore_0.1-5 foreach_1.3.0 codetools_0.2-2 [5] iterators_1.0.3 Biostrings_2.18.4 IRanges_1.8.9 biomaRt_2.6.0 loaded via a namespace (and not attached): [1] Biobase_2.10.0 RCurl_1.5-0 tools_2.12.0 XML_3.4-0

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ADD COMMENT • link updated 13.5 years ago by Steve Lianoglou ★ 13k • written 13.5 years ago by Ravi Karra ▴ 140

score 0 · Answer 1 · 2011-05-26

Hi, On Thu, May 26, 2011 at 6:51 PM, Ravi Karra <ravi.karra at="" gmail.com=""> wrote: > Hi, > I am trying to find TF binding sites in a set of promoters using position frequency matrices (pfm's) from jaspar and transfac. ?I have gotten this to work before on my machine at home, but cannot seem to get this to run on campus. ?I am not sure why I get the following error as I thought PWM can handle integer pfm's. ?Any thoughts? > > Thanks in advance, > Ravi > > Code: >> library (Biostrings) >> pfm > ?[,1] [,2] [,3] [,4] [,5] [,6] > A ? 13 ? ?0 ? 50 ? ?1 ? 13 ? ?6 > C ? 14 ? ?0 ? ?2 ? ?0 ? ?6 ? 16 > G ? 15 ? 53 ? ?0 ? ?1 ? 25 ? 22 > T ? 11 ? ?0 ? ?1 ? 51 ? ?9 ? ?9 >> typeof (pfm) > [1] "integer" >> pwm = pfm (PWM) > Error: could not find function "pfm" Were you just warming up your keyboard for the next step, or .. ? :-) >> library (Biostrings) >> pfm > ?[,1] [,2] [,3] [,4] [,5] [,6] > A ? 13 ? ?0 ? 50 ? ?1 ? 13 ? ?6 > C ? 14 ? ?0 ? ?2 ? ?0 ? ?6 ? 16 > G ? 15 ? 53 ? ?0 ? ?1 ? 25 ? 22 > T ? 11 ? ?0 ? ?1 ? 51 ? ?9 ? ?9 >> typeof (pfm) > [1] "integer" >> PWM (pfm) > Error in function (classes, fdef, mtable) ?: > ?unable to find an inherited method for function "PWM", for signature "matrix" >> sessionInfo () > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) I'm not sure what to say, but this works for me. You can look at the output of `showMethods('PWM'), R 2.13/bioc-2.8 has a PWM method defined for matrix objects: R> showMethods('PWM') Function: PWM (package Biostrings) x="character" x="DNAStringSet" x="matrix" Maybe you have to upgrade to the latest version of R/bioc? Sorry, I don't have a version of R 2.12 lying around to test further ... you say it worked for you at home, maybe your cpu at home is running R 2.13? HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact