Question: r3cseq error after finishing the work
0
gravatar for theodore.georgomanolis
4.0 years ago by
Germany

Hi all

After, successfully running a r3cseq I come across this warning:

Warning message:
In min(exp.filted$RPMs[exp.filted$rank <= round(0.01 * exp.max.rank)]) :
  no non-missing arguments to min; returning Inf

this is my script

#source("http://bioconductor.org/biocLite.R")
#library(r3Cseq)
#library(BSgenome.Hsapiens.UCSC.hg19)
my3Cseq.obj<-new("r3Cseq",organismName='hg19',isControlInvolved=FALSE,viewpoint_chromosome='chr6',alignedReadsBamExpFile="/media/trotos/4TB/WORK/Edn1_rep1_mem_sorted.bam",viewpoint_primer_forward='GCACTTGGGCTGAAGGATC',viewpoint_primer_reverse='TTGTTGTGTGCGGGGAATTT',expLabel="I15-1088-06-60_12_Edn1_rep1_mem_",restrictionEnzyme='ApoI')
getRawReads(my3Cseq.obj)
#expRawData(my3Cseq.obj)
getReadCountPerRestrictionFragment(my3Cseq.obj)
calculateRPM(my3Cseq.obj)
getInteractions(my3Cseq.obj)
#EDN1_rep1_Cross_60min<-expInteractionRegions(my3Cseq.obj)
viewpoint<-getViewpoint(my3Cseq.obj)
#plotOverviewInteractions(my3Cseq.obj)
generate3CseqReport(my3Cseq.obj)
rm(list = ls(all = TRUE))

Is it something to worry about?

Thank you all,

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] splines   stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.30.0                    r3Cseq_1.8.0                       sqldf_0.4-7.1                      RSQLite.extfuns_0.0.1              RSQLite_1.0.0                      DBI_0.3.1                          gsubfn_0.6-6                       proto_0.3-10                      
[10] RColorBrewer_1.1-2                 qvalue_1.36.0                      VGAM_0.9-8                         rtracklayer_1.22.7                 data.table_1.9.4                   Rsamtools_1.14.3                   Biostrings_2.30.1                  GenomicRanges_1.14.4               XVector_0.2.0                     
[19] IRanges_1.20.7                     BiocGenerics_0.8.0                 BiocInstaller_1.12.1              

loaded via a namespace (and not attached):
 [1] bitops_1.0-6   chron_2.3-47   magrittr_1.5   plyr_1.8.1     Rcpp_0.11.6    RCurl_1.95-4.7 reshape2_1.4.1 stringi_0.5-5  stringr_1.0.0  tcltk_3.0.2    tools_3.0.2    XML_3.98-1.3   zlibbioc_1.8.0

 

 

r3cseq 4c • 494 views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by theodore.georgomanolis0
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