Ah, yes, that method is better. I forgot to use it my example. - Dario.
---- Original message ---- >Date: Sat, 27 Aug 2011 13:53:16 +1000 >From: davis...@googlemail.com (on behalf of Davis McCarthy ><davis.mccar...@balliol.ox.ac.uk>) >Subject: Re: [Bioc-sig-seq] extract non-zero rows >To: d.strbe...@garvan.org.au >Cc: Estefania Mancini <estefania.manc...@indear.com>, >bioc-sig-sequencing@r-project.org > >Estefania and Dario > >A more efficient way to do this: >> row.positive.counts <- apply(dup.data$counts, 1, function(a.row) sum(a.row > >> 0)) > >would be this: >row.positive.counts <- rowSums( dup.data$counts > 0 ) > >You might prefer to use the functions rowSums(), rowMeans(), >colSums(), colMeans() instead of apply(), where you can. They are much >faster. > >Best wishes >Davis > > > >On 26 August 2011 10:00, Dario Strbenac <d.strbe...@garvan.org.au> wrote: >> Hi Estefania, >> >> If you want both columns to be non-zero, you should do >> > >> filtered <- dup.data[row.positive.counts == ncol(dup.data$counts), ] >> >> It makes a boolean vector for each row, then sums it, because TRUE is the >> same as 1, so the sum gives you how many columns are greater than zero. >> Then, the rows that have as many positive numbers as there are columns in >> the data frame are kept. >> >> To find unchanged genes, you might do >> >> unchanged <- dup.de.com$table[dup.de.com$table[, "logFC"] > -0.2 & >> dup.de.com$table[, "logFC"] < 0.2, ] >> >> replacing 0.2 with what you think the biggest fold change that unchanged >> genes might have. >> >> ---- Original message ---- >>>Date: Thu, 25 Aug 2011 11:39:03 -0300 (ART) >>>From: bioc-sig-sequencing-boun...@r-project.org (on behalf of Estefania >>>Mancini <estefania.manc...@indear.com>) >>>Subject: [Bioc-sig-seq] extract non-zero rows >>>To: bioc-sig-sequencing@r-project.org >>> >>>Dear all >>>I have loaded and analyzed properly 4 454 dataset, corresponding to control >>>and stress samples with their biological replicates. >>>I would like to know if is possible to filter, in my DGEList object >>> >>>-which tags dont have zero in any column, >>>-which of these tags could be consider "housekeeping" (at least with logFC >>>near 0) >>> >>>The object DGEList looks like this: >>> >>>>dup.data >>>An object of class "DGEList" >>>$samples >>> group lib.size norm.factors >>>A8_control control 77953 1 >>>A8_stress stress 176860 1 >>>mq_control control 98109 1 >>>mq_stress stress 145839 1 >>>pi_control control 132479 1 >>>pi_stress stress 142484 1 >>>tj_control control 65827 1 >>>tj_stress stress 144278 1 >>> >>>I have tried to filter using the suggested function: >>>>dup.de.filter <- dup.data[rowSums(dup.data$counts) >= 0, ] >>>or with >>>>dup.de.filter <- dup.data[rowSums(dup.data$counts) >= 1, ] >>>but have no changes at all. I have many rows which 0 and 1 read in some >>>column which should be excluded. >>> >>>Also: >>>dup.de.com >>>An object of class "DGEExact" >>>$table >>> logConc logFC p.value >>>Glyma13g11940.8 -2.588833 0.26176050 0.7348221 >>>Glyma13g11900.1 -2.875548 0.03020441 0.9688072 >>>Glyma09g24780.1 -3.501041 -0.12108619 0.8754371 >>>Glyma13g12050.1 -3.224648 0.03036675 0.9691009 >>>Glyma13g12070.1 -3.743064 0.14416487 0.8521188 >>>19860 more rows ... >>> >>>$comparison >>>[1] "control" "stress" >>>$genes >>>NULL >>> >>>Thanks in advance, >>>Estefania >>> >>>_______________________________________________ >>>Bioc-sig-sequencing mailing list >>>Bioc-sig-sequencing@r-project.org >>>https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> >> >> -------------------------------------- >> Dario Strbenac >> Research Assistant >> Cancer Epigenetics >> Garvan Institute of Medical Research >> Darlinghurst NSW 2010 >> Australia >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> Bioc-sig-sequencing@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
