Thank you very much. It is helpful. On Thu, Dec 19, 2013 at 1:33 PM, Hervé Pagès <hpages at="" fhcrc.org=""> wrote: > [Oops, forgot to Cc the list when I answered this. Sending it again...] > > > Hi Fabrice, > > The oligonucleotideFrequency() function in the Biostrings > package counts the nb of occurrences of all possible 5-mers > (use 'width=5') or 6-mers (use 'width=6'). You need to store > your sequence(s) in a DNAString or DNAStringSet object first. > On a DNAStringSet, the counts are returned in a matrix with 1 > row per sequence and 1 column per k-mer: > > library(Biostrings) > library(hgu95av2probe) > probes <- DNAStringSet(hgu95av2probe) > count5 <- oligonucleotideFrequency(probes, width=5) > > Then: > > > dim(count5) > [1] 201800 1024 > > count5[1:6, 1:10] > AAAAA AAAAC AAAAG AAAAT AAACA AAACC AAACG AAACT AAAGA AAAGC > [1,] 0 0 0 0 0 0 0 0 0 0 > [2,] 0 0 0 0 0 0 0 0 0 0 > [3,] 0 0 0 0 0 0 0 0 0 0 > [4,] 0 0 0 0 0 0 0 0 0 0 > [5,] 0 0 0 0 0 0 0 0 0 0 > [6,] 0 0 0 0 0 0 0 0 0 0 > > Maybe this function should have been called kmerFrequency()... > > Cheers, > H. > > > On 12/17/2013 10:28 AM, Fabrice Tourre wrote: >> >> Dear list, >> >> I have a list of bed regions. each region is 10bp length. I want to >> calculate the hexamers and pentamers in theses regions and get the >> zscore. Is there any existed packages to do this? >> >> Thank you very much in advance. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages at fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319

Julian, Thank you for your reply. For example, I have a sample fastq file. >chr1:14404-14435(-) GGCACA >chr1:14409-14440(-) AAAACG >chr1:14423-14454(-) AGAGGC >chr1:14424-14455(-) AAGAGG I want to calculate 6kmers in this sample file. Also I have extract a control fastq file. >chr1:14404-14435(-) CCTACA >chr1:14409-14440(-) TCGACG >chr1:14423-14454(-) TCAGAT >chr1:14424-14455(-) CAAGGC The z-score was calculated for each pentamer as: (occurrence in sequences ? average occurrence in control sequences) / standard deviation of occurrence in control sequences On Wed, Dec 18, 2013 at 4:07 AM, Julian Gehring <julian.gehring at="" embl.de=""> wrote: > > > Hi Fabrice, > > Could you give an example for this, especially on what the z-score > statistics is about to tell you? > > Best wishes > Julian > > > > On 12/17/2013 07:28 PM, Fabrice Tourre wrote: >> >> Dear list, >> >> I have a list of bed regions. each region is 10bp length. I want to >> calculate the hexamers and pentamers in theses regions and get the >> zscore. Is there any existed packages to do this? >> >> Thank you very much in advance. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ at public.gmane.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >

Julian, Thank you for your reply. For example, I have a sample fastq file. >chr1:14404-14435(-) GGCACA >chr1:14409-14440(-) AAAACG >chr1:14423-14454(-) AGAGGC >chr1:14424-14455(-) AAGAGG I want to calculate 6kmers in this sample file. Also I have extract a control fastq file. >chr1:14404-14435(-) CCTACA >chr1:14409-14440(-) TCGACG >chr1:14423-14454(-) TCAGAT >chr1:14424-14455(-) CAAGGC The z-score was calculated for each pentamer as: (occurrence in sequences ? average occurrence in control sequences) / standard deviation of occurrence in control sequences On Wed, Dec 18, 2013 at 4:07 AM, Julian Gehring <julian.gehring at="" embl.de=""> wrote: > > > Hi Fabrice, > > Could you give an example for this, especially on what the z-score > statistics is about to tell you? > > Best wishes > Julian > > > > On 12/17/2013 07:28 PM, Fabrice Tourre wrote: >> >> Dear list, >> >> I have a list of bed regions. each region is 10bp length. I want to >> calculate the hexamers and pentamers in theses regions and get the >> zscore. Is there any existed packages to do this? >> >> Thank you very much in advance. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor-0bNBQ1PAWB4BXFe83j6qeQ at public.gmane.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >