Assuming that chr1 is the first sequence in yopur bpmap file (beware, sometimes the first sequences are spike-in controls), it should be as simple as bpmap = readBpmap(FILE) writeTpmap(filename = "tmp.tpmap", bpmaplist = bpmap[1]) # note just single [ so you geta list with one component tpmap2bpmap(tmpmapname = "tmp.tpmap", bpmapname = "tmp.bpmap") tpmap2bpmap converts from a text based bpmap file (which according to Affy's documentation is called a tpmap file, but I have never seen that term used outside of their documentation) into a binary bpmap. In case you wonder "tpmap" = "text probe map" and bpmap = "binary probe map" Kasper On Dec 4, 2008, at 16:48 , Mark Robinson wrote: > Hi Arnaud. > > I suspect the 'writeTpmap' and 'tpmap2bpmap' functions in the > 'affxparser' package would be useful for this, though I haven't done > it myself ... > > > library(affxparser) > > ?tpmap2bpmap > > ?writeTpmap > > You can use 'readBpmap' to read in your original BPMAP file into a > list. > > HTH. > Mark > > On 05/12/2008, at 7:56 AM, Droit Arnaud wrote: > >> Hello all, >> >> I have a BPMAP file (89 Mo) and the size is too big for the >> bioconductor?s guideline. I have some alternative as to create a >> separate package for the data. >> But, first, I am thinking to reduce the size of the file by >> removing data from the BPMAP file. >> I want to extract data from BPMAP file (e.g. all data for chr1) and >> rebuild BPMAP file with only data from chr1, >> and I am just wondering if anyone knows if it is possible to >> rebuild BPMAP files. >> >> Thank you >> >> Arnaud Droit. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > ------------------------------ > Mark Robinson > Epigenetics Laboratory, Garvan > Bioinformatics Division, WEHI > e: m.robinson at garvan.org.au > e: mrobinson at wehi.edu.au > p: +61 (0)3 9345 2628 > f: +61 (0)3 9347 0852 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor