Dear Jens, Thanks for the feedback! Maxgap does not appply when output = nearestStart, which is the default setting. Maxgap applies when you set output = overlapping, as shown below. annotatePeakInBatch(a, AnnotationData = g, output="overlapping", maxgap=10) annotatePeakInBatch(a, AnnotationData = g, output="overlapping", maxgap=40) annotatePeakInBatch(a, AnnotationData = g, output="overlapping", maxgap=400) For more options to call annotatePeakInBatch, please type ?annotatePeakInBatch in a R session. I am ccing bioconductor list so others with similar questions can benefit. Best regards, Julie ******************************************* Lihua Julie Zhu, Ph.D Research Associate Professor Program in Gene Function and Expression Program in Bioinformatics and Integrative Biology Program in Molecular Medicine University of Massachusetts Medical School 364 Plantation Street, Room 613 Worcester, MA 01605 508-856-5256 http://profiles.umassmed.edu/profiles/ProfileDetails.aspx?From=SE&Pers on=1134 On 8/11/14 9:03 AM, "Preussner, Jens" <jens.preussner@mpi-bn.mpg.de> wrote: Dear Julie, I have some issues with the maxgap option when using the annotatePeakInBatch function of your ChIPpeakAnno package in R. It seems that the maxgap option is ignored. Suppose I have two bed files, the first one defining a peak between 1050 and 1100 on chr1, the latter defining a gene from 500 to 1000, also on chr1. Running annotatePeakInBatch with maxgap=40 still returns the interval. Please find attached two files, a.bed and g.bed, and the corresponding R code that I used to run it. Thank you for a short answer, Best, Jens Jens Preußner Bioinformatics Service Max Planck Institute for Heart and Lung Research Ludwigstrasse 43 – FGI – 61231 Bad Nauheim Germany R-Code: require('ChIPpeakAnno') a = BED2RangedData(file.path("a.bed")) g = BED2RangedData(file.path("g.bed")) annotatePeakInBatch(a, AnnotationData = g, maxgap=10) annotatePeakInBatch(a, AnnotationData = g, maxgap=40) [[alternative HTML version deleted]]

Jens, As more parameters added over the years, it gets easier to miss some of the parameters. I myself often consult the help page using ?annotatePeakInBatch. For future correspondence, could you please cc bioconductor list? Many thanks! Best regards, Julie On 8/11/14 9:35 AM, "Preussner, Jens" <jens.preussner@mpi-bn.mpg.de> wrote: Hi Julie, I totally missed this little piece of information :) Thank you a lot! Best, Jens From: Zhu, Lihua (Julie) [mailto:Julie.Zhu@umassmed.edu] Sent: Montag, 11. August 2014 15:33 To: Preussner, Jens Cc: bioconductor@r-project.org Subject: Re: ChIPpeakAnno: Maxgap option in annotatePeakInBatch Dear Jens, Thanks for the feedback! Maxgap does not appply when output = nearestStart, which is the default setting. Maxgap applies when you set output = overlapping, as shown below. annotatePeakInBatch(a, AnnotationData = g, output="overlapping", maxgap=10) annotatePeakInBatch(a, AnnotationData = g, output="overlapping", maxgap=40) annotatePeakInBatch(a, AnnotationData = g, output="overlapping", maxgap=400) For more options to call annotatePeakInBatch, please type ?annotatePeakInBatch in a R session. I am ccing bioconductor list so others with similar questions can benefit. Best regards, Julie ******************************************* Lihua Julie Zhu, Ph.D Research Associate Professor Program in Gene Function and Expression Program in Bioinformatics and Integrative Biology Program in Molecular Medicine University of Massachusetts Medical School 364 Plantation Street, Room 613 Worcester, MA 01605 508-856-5256 http://profiles.umassmed.edu/profiles/ProfileDetails.aspx?From=SE&Pers on=1134 On 8/11/14 9:03 AM, "Preussner, Jens" <jens.preussner@mpi-bn.mpg.de> wrote: Dear Julie, I have some issues with the maxgap option when using the annotatePeakInBatch function of your ChIPpeakAnno package in R. It seems that the maxgap option is ignored. Suppose I have two bed files, the first one defining a peak between 1050 and 1100 on chr1, the latter defining a gene from 500 to 1000, also on chr1. Running annotatePeakInBatch with maxgap=40 still returns the interval. Please find attached two files, a.bed and g.bed, and the corresponding R code that I used to run it. Thank you for a short answer, Best, Jens Jens Preußner Bioinformatics Service Max Planck Institute for Heart and Lung Research Ludwigstrasse 43 – FGI – 61231 Bad Nauheim Germany R-Code: require('ChIPpeakAnno') a = BED2RangedData(file.path("a.bed")) g = BED2RangedData(file.path("g.bed")) annotatePeakInBatch(a, AnnotationData = g, maxgap=10) annotatePeakInBatch(a, AnnotationData = g, maxgap=40) [[alternative HTML version deleted]]