On Jul 11, 2012, at 10:21 AM, Kasper Daniel Hansen wrote: > What you are reporting is true for any (well, there may be exceptions > I guess) subsetting. Try for example with a standard matrix. The > solution is to add which(). Contrast > >> x = c(1,2,NA) >> x == 2 > [1] FALSE TRUE NA >> which(x == 2) > [1] 2 > > Kasper > Thanks, I should have tried that before. This syntax works: > tss.annot.gr[na.omit(which(elementMetadatatss.annot.gr) $GENE>0)),"GENE"] GRanges with 3446 ranges and 1 elementMetadata col: seqnames ranges strand | GENE <rle> <iranges> <rle> | <numeric> [1] chr1 [ 4773791, 4776291] - | 1.063973966 [2] chr1 [ 5007460, 5009960] - | 1.668134677 [3] chr1 [16092486, 16094986] - | 1.748685661 [4] chr1 [36737931, 36740431] - | 1.465666717 [5] chr1 [38052053, 38054553] - | 1.750940655 [6] chr1 [38054354, 38056854] + | 1.677518675 [7] chr1 [39592146, 39594646] + | 0.696900841 [8] chr1 [40380974, 40383474] + | 0.777552281 [9] chr1 [40738056, 40740556] + | 0.511665769 Mike > On Wed, Jul 11, 2012 at 11:09 AM, Michael Muratet > <mmuratet at="" hudsonalpha.org=""> wrote: >> Greetings >> >> I would like to select elements from a GRanges object by testing >> values in >> the metadata columns. This seems to work OK: >> >> x.gr[which(elementMetadatax.gr)$fdr<0.05)] >> >> So does this, although there's nothing in the documentation about >> the [] >> operator accepting logical values: >> >> fosl2.th17.gr[elementMetadatafosl2.th17.gr)$fdr<0.05] >> >> The problem arises when I try to select from a GRanges object where >> the >> metadata columns have NAs: >> >>> tss.annot.gr[na.omit(elementMetadatatss.annot.gr)$GENE>0),"GENE"] >> GRanges with 4028 ranges and 1 elementMetadata col: >> seqnames ranges strand | GENE >> <rle> <iranges> <rle> | <numeric> >> [1] chr1 [ 3659579, 3662079] - | <na> >> [2] chr1 [ 4847394, 4849894] + | 0 >> [3] chr1 [10025979, 10028479] - | <na> >> [4] chr1 [17085879, 17088379] - | <na> >> [5] chr1 [21067298, 21069798] - | <na> >> [6] chr1 [21949662, 21952162] - | 0 >> [7] chr1 [23388014, 23390514] - | <na> >> [8] chr1 [23768264, 23770764] + | <na> >> [9] chr1 [23927128, 23929628] - | <na> >> ... ... ... ... ... ... >> [4020] chr2 [126607180, 126609680] - | 0 >> [4021] chr2 [127345106, 127347606] - | 0 >> [4022] chr2 [129195132, 129197632] + | -1.223140339 >> [4023] chr2 [129194856, 129197356] - | -1.628782357 >> [4024] chr2 [129360338, 129362838] - | -1.475535653 >> [4025] chr2 [129837609, 129840109] + | 0 >> [4026] chr2 [129948520, 129951020] + | 0 >> [4027] chr2 [140213446, 140215946] - | 0 >> [4028] chr2 [148267271, 148269771] - | -1.564551101 >> >> The values returned violate the condition. It won't work at all >> without >> na.omit. >> >> I can coerce the GRanges object to a data.frame, do the selection >> and create >> a new GRanges object, but I'm hoping there is a way to do it >> directly. >> >> Am I using the syntax correctly? Is there something peculiar about a >> DataFrame vs a data.frame that's getting in the way? >> >> Thanks >> >> Mike >> >> >> >> Michael Muratet, Ph.D. >> Senior Scientist >> HudsonAlpha Institute for Biotechnology >> mmuratet at hudsonalpha.org >> (256) 327-0473 (p) >> (256) 327-0966 (f) >> >> Room 4005 >> 601 Genome Way >> Huntsville, Alabama 35806 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor Michael Muratet, Ph.D. Senior Scientist HudsonAlpha Institute for Biotechnology mmuratet at hudsonalpha.org (256) 327-0473 (p) (256) 327-0966 (f) Room 4005 601 Genome Way Huntsville, Alabama 35806