Hi there! According to the documentation, the "isUnmappedQuery" should be set to FALSE if I want to obtain only unmapped reads and to TRUE if I am only interested in mapped reads. However I find that it works exactly the other way around. I.e. executing: y <- scanBam(file, param=ScanBamParam(what=c("qname"), flag=scanBamFlag(isUnmappedQuery=TRUE)))) and grepping for the returned query-names in the bamfile itself I find only reads that are not mapped, whereas changing the isUnmappedQuery to FALSE i get reads that indeed are mapped. This is exactly opposite to what the documentation states: "isUnmappedQuery: A logical(1) indicating whether unmapped (FALSE), mapped (TRUE), or any (NA) read should be returned." I am thus assuming there is a mistake in either the documentation or the code. Which one is it? (Or, am I just doing something wrong and not w/o it?) Cheers Thomas ---------- > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Rsamtools_1.0.5 Biostrings_2.16.6 GenomicRanges_1.0.5 [4] IRanges_1.6.8 loaded via a namespace (and not attached): [1] Biobase_2.8.0

On 07/19/2010 09:49 AM, Thomas Unterthiner wrote: > Hi there! > > According to the documentation, the "isUnmappedQuery" should be set to > FALSE if I want to obtain only unmapped reads and to TRUE if I am only > interested in mapped reads. However I find that it works exactly the > other way around. > > I.e. executing: > > y <- scanBam(file, param=ScanBamParam(what=c("qname"), > flag=scanBamFlag(isUnmappedQuery=TRUE)))) > > and grepping for the returned query-names in the bamfile itself I find > only reads that are not mapped, whereas changing the isUnmappedQuery to > FALSE i get reads that indeed are mapped. This is exactly opposite to > what the documentation states: > > "isUnmappedQuery: A logical(1) indicating whether unmapped (FALSE), > mapped (TRUE), or any (NA) read should be returned." > > > I am thus assuming there is a mistake in either the documentation or the > code. Which one is it? (Or, am I just doing something wrong and not w/o > it?) It's a documentation error, should be fixed when 1.0.6 reaches biocLite() in 24-36 hours. Thanks for the report. Martin > > Cheers > > Thomas > > > ---------- >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-pc-linux-gnu > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 > [7] LC_PAPER=en_US.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Rsamtools_1.0.5 Biostrings_2.16.6 GenomicRanges_1.0.5 > [4] IRanges_1.6.8 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793