Searching for data in data.frames

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J.delasHeras@ed.ac.uk ★ 1.9k

@jdelasherasedacuk-1189

Last seen 9.3 years ago

United Kingdom

This may be a very basic question, but I am looking in the R manual and I haven't found the right function... and I am sure it must exist already. So I apologise in advance if I seem to be blind or missing something! :) What I am after is very simple. I am using Limma and I have a number of data frames (RGList, MAList, MArrayLM...). Sometimes I just want to locate the data for a particular gene, or where a particular value for M occurs, etc. I want to find, for instance, all occurrences of "COL6A3" in RG$genes, and return the position of those occurrences, for instance 345, 7840, 15003. Then I can use that information to give me the foreground intensities corresponding to that gene for any given slide. I came across the function "subset" which seems like it would serve my purpose (or could be adapted to serve my purpose), but I get errors no matter what I do... I appreciate this must be a pretty basic question, but... I have spent the last hour searching for this and so far no luck. I was going to just write a simple search function, but there must be already a function already defined. Thanks! Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK

limma limma • 807 views

ADD COMMENT • link updated 18.7 years ago by Stephen Henderson ★ 1.0k • written 18.7 years ago by J.delasHeras@ed.ac.uk ★ 1.9k

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michael watson IAH-C ★ 3.4k

@michael-watson-iah-c-378

Last seen 10.3 years ago

Try my.data.frame[grep("search term", my.data.frame$column.name),] -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of J.delasHeras at ed.ac.uk Sent: 21 April 2006 14:55 To: bioconductor at stat.math.ethz.ch Subject: [BioC] Searching for data in data.frames This may be a very basic question, but I am looking in the R manual and I haven't found the right function... and I am sure it must exist already. So I apologise in advance if I seem to be blind or missing something! :) What I am after is very simple. I am using Limma and I have a number of data frames (RGList, MAList, MArrayLM...). Sometimes I just want to locate the data for a particular gene, or where a particular value for M occurs, etc. I want to find, for instance, all occurrences of "COL6A3" in RG$genes, and return the position of those occurrences, for instance 345, 7840, 15003. Then I can use that information to give me the foreground intensities corresponding to that gene for any given slide. I came across the function "subset" which seems like it would serve my purpose (or could be adapted to serve my purpose), but I get errors no matter what I do... I appreciate this must be a pretty basic question, but... I have spent the last hour searching for this and so far no luck. I was going to just write a simple search function, but there must be already a function already defined. Thanks! Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK _______________________________________________ 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

ADD COMMENT • link 18.7 years ago michael watson IAH-C ★ 3.4k

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Aha! thanks a lot! grep and regexpr were the type of functions I was looking for. Jose Quoting "michael watson (IAH-C)" <michael.watson at="" bbsrc.ac.uk="">: > Try > > my.data.frame[grep("search term", my.data.frame$column.name),] > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > J.delasHeras at ed.ac.uk > Sent: 21 April 2006 14:55 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Searching for data in data.frames > > > This may be a very basic question, but I am looking in the R manual and > I haven't found the right function... and I am sure it must exist > already. So I apologise in advance if I seem to be blind or missing > something! :) > > What I am after is very simple. I am using Limma and I have a number of > data frames (RGList, MAList, MArrayLM...). Sometimes I just want to > locate the data for a particular gene, or where a particular value for M > occurs, etc. > > I want to find, for instance, all occurrences of "COL6A3" in RG$genes, > and return the position of those occurrences, for instance 345, 7840, > 15003. Then I can use that information to give me the foreground > intensities corresponding to that gene for any given slide. > > I came across the function "subset" which seems like it would serve my > purpose (or could be adapted to serve my purpose), but I get errors no > matter what I do... > > I appreciate this must be a pretty basic question, but... I have spent > the last hour searching for this and so far no luck. I was going to just > write a simple search function, but there must be already a function > already defined. > > Thanks! > > Jose > > -- > Dr. Jose I. de las Heras Email: > J.delasHeras at ed.ac.uk > The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 > Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 > Swann Building, Mayfield Road > University of Edinburgh > Edinburgh EH9 3JR > UK > > _______________________________________________ > 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 > > -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK

ADD REPLY • link 18.7 years ago J.delasHeras@ed.ac.uk ★ 1.9k

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Stephen Henderson ★ 1.0k

@stephen-henderson-71

Last seen 7.7 years ago

Have you tried wh<-which(RG$genes=="COL6A3") Stephen Henderson Wolfson Inst. for Biomedical Research Cruciform Bldg., Gower Street University College London United Kingdom, WC1E 6BT +44 (0)207 679 6827 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of J.delasHeras at ed.ac.uk Sent: 21 April 2006 14:55 To: bioconductor at stat.math.ethz.ch Subject: [BioC] Searching for data in data.frames This may be a very basic question, but I am looking in the R manual and I haven't found the right function... and I am sure it must exist already. So I apologise in advance if I seem to be blind or missing something! :) What I am after is very simple. I am using Limma and I have a number of data frames (RGList, MAList, MArrayLM...). Sometimes I just want to locate the data for a particular gene, or where a particular value for M occurs, etc. I want to find, for instance, all occurrences of "COL6A3" in RG$genes, and return the position of those occurrences, for instance 345, 7840, 15003. Then I can use that information to give me the foreground intensities corresponding to that gene for any given slide. I came across the function "subset" which seems like it would serve my purpose (or could be adapted to serve my purpose), but I get errors no matter what I do... I appreciate this must be a pretty basic question, but... I have spent the last hour searching for this and so far no luck. I was going to just write a simple search function, but there must be already a function already defined. Thanks! Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK _______________________________________________ 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 ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}

ADD COMMENT • link 18.7 years ago Stephen Henderson ★ 1.0k

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Quoting Stephen Henderson <s.henderson at="" ucl.ac.uk="">: > Have you tried > > wh<-which(RG$genes=="COL6A3") aha!!! THIS is EXACTLY what I was searching for. while the other functions are also very helpful (grep and regexpr), "which" is *exactly* what I wanted. Perfect! Thank you, Stephen! Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK

ADD REPLY • link 18.7 years ago J.delasHeras@ed.ac.uk ★ 1.9k

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