[BioC] CHARM - plotDMRs
Andrew Beggs
a.beggs at bham.ac.uk
Thu Nov 8 14:02:53 CET 2012
Okay I have solved the problem, sorry I was stupid! Didn't realise I needed to specify four colours for the four regions!
BW
Andrew
-----Original Message-----
From: Andrew Beggs [guest] [mailto:guest at bioconductor.org]
Sent: 08 November 2012 12:49
To: bioconductor at r-project.org; a.beggs at bham.ac.uk
Cc: charm Maintainer
Subject: CHARM - plotDMRs
Hello
I was wondering if anyone can help. I have a 4 group exposure for my methylation array experiments, groups one, two, three and four
I have used:
plotDMRs(dmrs=thedmrs, Genome=Hsapiens, cpg.islands=cpg.cur, exposure=pd$tissue,outfile="./group1-group2.pdf", which_plot=c(1),which_points=c("group1","group2"), smoo="loess", ADD=3000,cols=c("black","red","blue"))
To try and plot Group 1 against group 2. However I get:
Error: length(cols) >= length(unique(exposure)) is not TRUE
I am using the following to generate the DMRs, and finds 125 DMRs:
thedmrs = dmrFind(p=p, mod=mod, mod0=mod0, coeff=2, pns=pns, chr=chr, pos=pos)
And the output I get is:
Running SVA
Number of significant surrogate variables is: 10 Iteration (out of 5 ):1 2 3 4 5 Regression Obtaining estimates for factor(pd$tissue, levels = c("group1", "group2", "group3", "group4"))group2 Smoothing ================================================================================
...................................................
Covariate recognized as categorical.
Found 125 potential DMRs
Can anyone help?
-- output of sessionInfo():
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] corpcor_1.6.4 BSgenome.Hsapiens.UCSC.hg18_1.3.19
[3] BSgenome_1.26.1 Biostrings_2.26.2
[5] GenomicRanges_1.10.3 IRanges_1.16.4
[7] pd.2006.11.02.hg18.cpg.promo_0.0.1 oligo_1.22.0
[9] oligoClasses_1.20.0 RSQLite_0.11.2
[11] DBI_0.2-5 charm_2.4.0
[13] genefilter_1.40.0 RColorBrewer_1.0-5
[15] fields_6.7 spam_0.29-2
[17] SQN_1.0.5 nor1mix_1.1-3
[19] mclust_4.0 Biobase_2.18.0
[21] BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] affxparser_1.30.0 affyio_1.26.0 annotate_1.36.0
[4] AnnotationDbi_1.20.2 BiocInstaller_1.8.3 bit_1.1-9
[7] codetools_0.2-8 ff_2.2-9 foreach_1.4.0
[10] gtools_2.7.0 iterators_1.0.6 limma_3.14.1
[13] MASS_7.3-22 multtest_2.14.0 parallel_2.15.2
[16] preprocessCore_1.20.0 siggenes_1.32.0 splines_2.15.2
[19] stats4_2.15.2 survival_2.36-14 sva_3.4.0
[22] tools_2.15.2 XML_3.95-0.1 xtable_1.7-0
[25] zlibbioc_1.4.0
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